Starting phenix.real_space_refine on Sun Aug 24 10:41:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hlp_34880/08_2025/8hlp_34880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hlp_34880/08_2025/8hlp_34880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hlp_34880/08_2025/8hlp_34880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hlp_34880/08_2025/8hlp_34880.map" model { file = "/net/cci-nas-00/data/ceres_data/8hlp_34880/08_2025/8hlp_34880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hlp_34880/08_2025/8hlp_34880.cif" } resolution = 3.5 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 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= 0.001 sd= 0.067 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 1 5.49 5 S 95 5.16 5 C 12423 2.51 5 N 3113 2.21 5 O 3433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19067 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 10151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 10151 Classifications: {'peptide': 1253} Link IDs: {'PTRANS': 40, 'TRANS': 1212} Chain breaks: 8 Chain: "F" Number of atoms: 7352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7352 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 36, 'TRANS': 878} Chain breaks: 7 Chain: "C" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1297 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 8, 'TRANS': 155} Chain breaks: 2 Chain: "A" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 197 Unusual residues: {' CA': 2, '3PE': 2, 'R16': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1, '3PE:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.35, per 1000 atoms: 0.23 Number of scatterers: 19067 At special positions: 0 Unit cell: (169.52, 117.52, 183.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 95 16.00 P 1 15.00 O 3433 8.00 N 3113 7.00 C 12423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " distance=2.03 Simple disulfide: pdb=" SG CYS F 303 " - pdb=" SG CYS F1044 " distance=2.03 Simple disulfide: pdb=" SG CYS F 354 " - pdb=" SG CYS F1059 " distance=2.03 Simple disulfide: pdb=" SG CYS F 904 " - pdb=" SG CYS F 974 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG F1101 " - " ASN F 468 " " NAG F1102 " - " ASN F 324 " " NAG F1103 " - " ASN F 92 " " NAG F1104 " - " ASN F 184 " " NAG F1105 " - " ASN F 895 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 817.2 milliseconds Enol-peptide restraints added in 1.4 microseconds 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 14 sheets defined 57.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.695A pdb=" N ILE A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 121 " --> pdb=" O CYS A 117 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU A 122 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 143 removed outlier: 3.743A pdb=" N ALA A 142 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 180 removed outlier: 3.656A pdb=" N SER A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 211 removed outlier: 3.603A pdb=" N TRP A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.501A pdb=" N ARG A 240 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 242 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 251 removed outlier: 3.590A pdb=" N LEU A 247 " --> pdb=" O ARG A 243 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.781A pdb=" N GLN A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 290 removed outlier: 4.481A pdb=" N ILE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 349 through 361 Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.936A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 418 removed outlier: 3.669A pdb=" N PHE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 445 removed outlier: 3.565A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 441 " --> pdb=" O TYR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 removed outlier: 4.008A pdb=" N LYS A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 543 Processing helix chain 'A' and resid 549 through 578 removed outlier: 3.796A pdb=" N GLU A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.671A pdb=" N SER A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 609 Processing helix chain 'A' and resid 612 through 627 Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 635 through 674 removed outlier: 5.156A pdb=" N ARG A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER A 650 " --> pdb=" O ASN A 646 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 654 " --> pdb=" O SER A 650 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 705 removed outlier: 3.934A pdb=" N LEU A 697 " --> pdb=" O PRO A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 729 through 778 removed outlier: 3.528A pdb=" N PHE A 733 " --> pdb=" O VAL A 729 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS A 767 " --> pdb=" O THR A 763 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A 768 " --> pdb=" O SER A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 919 removed outlier: 4.085A pdb=" N ASN A 904 " --> pdb=" O THR A 900 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 917 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 919 " --> pdb=" O ILE A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 972 removed outlier: 3.984A pdb=" N GLU A 967 " --> pdb=" O ILE A 943 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET A 972 " --> pdb=" O ILE A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1008 removed outlier: 3.841A pdb=" N LEU A 994 " --> pdb=" O ASN A 990 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A1008 " --> pdb=" O PHE A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1010 No H-bonds generated for 'chain 'A' and resid 1009 through 1010' Processing helix chain 'A' and resid 1011 through 1012 No H-bonds generated for 'chain 'A' and resid 1011 through 1012' Processing helix chain 'A' and resid 1013 through 1021 removed outlier: 4.204A pdb=" N LEU A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1025 Proline residue: A1025 - end of helix No H-bonds generated for 'chain 'A' and resid 1022 through 1025' Processing helix chain 'A' and resid 1026 through 1032 removed outlier: 3.944A pdb=" N ASN A1030 " --> pdb=" O LEU A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1071 removed outlier: 4.992A pdb=" N ASN A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE A1052 " --> pdb=" O THR A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1120 through 1133 Processing helix chain 'A' and resid 1136 through 1145 removed outlier: 3.627A pdb=" N LEU A1140 " --> pdb=" O GLY A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1161 No H-bonds generated for 'chain 'A' and resid 1159 through 1161' Processing helix chain 'A' and resid 1162 through 1173 removed outlier: 3.655A pdb=" N PHE A1166 " --> pdb=" O ILE A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1194 Processing helix chain 'A' and resid 1195 through 1197 No H-bonds generated for 'chain 'A' and resid 1195 through 1197' Processing helix chain 'A' and resid 1203 through 1212 removed outlier: 3.717A pdb=" N ARG A1207 " --> pdb=" O ASP A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1215 No H-bonds generated for 'chain 'A' and resid 1213 through 1215' Processing helix chain 'A' and resid 1226 through 1238 removed outlier: 3.716A pdb=" N VAL A1232 " --> pdb=" O HIS A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1259 removed outlier: 4.140A pdb=" N GLN A1259 " --> pdb=" O CYS A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1293 Processing helix chain 'A' and resid 1294 through 1299 Processing helix chain 'A' and resid 1301 through 1321 removed outlier: 3.527A pdb=" N LEU A1309 " --> pdb=" O VAL A1305 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1310 " --> pdb=" O PHE A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1383 removed outlier: 4.405A pdb=" N VAL A1381 " --> pdb=" O ARG A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1391 removed outlier: 3.860A pdb=" N LEU A1388 " --> pdb=" O LEU A1384 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A1390 " --> pdb=" O LYS A1386 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY A1391 " --> pdb=" O LEU A1387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1384 through 1391' Processing helix chain 'A' and resid 1391 through 1408 Processing helix chain 'A' and resid 1408 through 1430 removed outlier: 4.067A pdb=" N ALA A1412 " --> pdb=" O LEU A1408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1462 Processing helix chain 'A' and resid 1465 through 1474 Processing helix chain 'A' and resid 1499 through 1526 Processing helix chain 'A' and resid 1526 through 1531 Processing helix chain 'A' and resid 1538 through 1553 Processing helix chain 'A' and resid 1582 through 1584 No H-bonds generated for 'chain 'A' and resid 1582 through 1584' Processing helix chain 'A' and resid 1585 through 1593 Processing helix chain 'A' and resid 1608 through 1618 removed outlier: 3.664A pdb=" N LEU A1618 " --> pdb=" O VAL A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1632 Processing helix chain 'A' and resid 1633 through 1638 Processing helix chain 'F' and resid 29 through 53 Processing helix chain 'F' and resid 53 through 64 removed outlier: 3.762A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 110 removed outlier: 3.687A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 187 Processing helix chain 'F' and resid 188 through 200 removed outlier: 4.139A pdb=" N VAL F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP F 200 " --> pdb=" O ASN F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 241 through 249 removed outlier: 4.214A pdb=" N GLY F 247 " --> pdb=" O TRP F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 265 Processing helix chain 'F' and resid 266 through 281 removed outlier: 3.545A pdb=" N LYS F 270 " --> pdb=" O GLY F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'F' and resid 332 through 344 Processing helix chain 'F' and resid 345 through 350 removed outlier: 5.578A pdb=" N ASN F 348 " --> pdb=" O LEU F 345 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER F 350 " --> pdb=" O TYR F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 376 Processing helix chain 'F' and resid 396 through 406 removed outlier: 3.609A pdb=" N ASN F 406 " --> pdb=" O MET F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 424 removed outlier: 4.011A pdb=" N GLN F 424 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 431 removed outlier: 3.707A pdb=" N VAL F 429 " --> pdb=" O GLU F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 437 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 560 through 565 removed outlier: 3.650A pdb=" N GLU F 565 " --> pdb=" O PHE F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 580 removed outlier: 3.610A pdb=" N VAL F 572 " --> pdb=" O ASN F 568 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU F 573 " --> pdb=" O ASP F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 648 removed outlier: 3.958A pdb=" N LEU F 648 " --> pdb=" O TYR F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 651 No H-bonds generated for 'chain 'F' and resid 649 through 651' Processing helix chain 'F' and resid 652 through 657 Processing helix chain 'F' and resid 675 through 690 Processing helix chain 'F' and resid 699 through 719 Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 757 through 760 Processing helix chain 'F' and resid 761 through 770 Processing helix chain 'F' and resid 817 through 827 removed outlier: 3.589A pdb=" N TRP F 821 " --> pdb=" O ASP F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 864 through 870 removed outlier: 3.660A pdb=" N GLN F 870 " --> pdb=" O ASP F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 879 through 887 removed outlier: 3.826A pdb=" N MET F 883 " --> pdb=" O ASP F 879 " (cutoff:3.500A) Processing helix chain 'F' and resid 888 through 890 No H-bonds generated for 'chain 'F' and resid 888 through 890' Processing helix chain 'F' and resid 1042 through 1047 removed outlier: 3.509A pdb=" N MET F1046 " --> pdb=" O ASN F1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 257 removed outlier: 3.786A pdb=" N ASP C 244 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 312 removed outlier: 4.108A pdb=" N SER C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 332 removed outlier: 3.913A pdb=" N LEU C 330 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 358 removed outlier: 4.093A pdb=" N LEU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY C 358 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 375 removed outlier: 4.252A pdb=" N ALA C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA C 372 " --> pdb=" O GLN C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 383 Processing helix chain 'C' and resid 391 through 403 removed outlier: 3.607A pdb=" N HIS C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR C 402 " --> pdb=" O HIS C 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 297 through 300 removed outlier: 3.756A pdb=" N THR A 297 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1077 through 1078 removed outlier: 3.793A pdb=" N GLU A1112 " --> pdb=" O THR A1077 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1092 through 1096 Processing sheet with id=AA4, first strand: chain 'F' and resid 69 through 72 Processing sheet with id=AA5, first strand: chain 'F' and resid 125 through 126 removed outlier: 6.733A pdb=" N TYR F 125 " --> pdb=" O VAL F 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 205 through 210 removed outlier: 4.458A pdb=" N TRP F 205 " --> pdb=" O ASP F 491 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL F 487 " --> pdb=" O GLY F 209 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY F 486 " --> pdb=" O VAL F 466 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET F 488 " --> pdb=" O LEU F 464 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR F 450 " --> pdb=" O VAL F 459 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 298 through 300 removed outlier: 3.559A pdb=" N PHE F 294 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU F 257 " --> pdb=" O PHE F 361 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE F 358 " --> pdb=" O PHE F 385 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE F 387 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL F 384 " --> pdb=" O TYR F 409 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N TYR F 411 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 521 through 522 removed outlier: 3.574A pdb=" N TYR F 511 " --> pdb=" O VAL F 622 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 513 " --> pdb=" O ALA F 620 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 741 through 743 removed outlier: 3.759A pdb=" N ALA F 731 " --> pdb=" O LYS F 815 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL F 812 " --> pdb=" O LYS F 796 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 800 through 801 Processing sheet with id=AB2, first strand: chain 'F' and resid 858 through 862 removed outlier: 6.490A pdb=" N LEU F 859 " --> pdb=" O ASP F 854 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASP F 854 " --> pdb=" O LEU F 859 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET F1017 " --> pdb=" O HIS F1004 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS F1004 " --> pdb=" O MET F1017 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE F1003 " --> pdb=" O GLY F 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY F 992 " --> pdb=" O PHE F1003 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 893 through 895 removed outlier: 3.586A pdb=" N PHE F 982 " --> pdb=" O ALA F 893 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN F 980 " --> pdb=" O ASN F 895 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 899 through 903 removed outlier: 5.692A pdb=" N TYR F 900 " --> pdb=" O THR F 976 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR F 976 " --> pdb=" O TYR F 900 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE F 975 " --> pdb=" O SER F1038 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN F1036 " --> pdb=" O GLU F 977 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 230 through 232 removed outlier: 6.647A pdb=" N VAL C 231 " --> pdb=" O VAL C 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 915 hydrogen bonds defined for protein. 2670 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: 4.21 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3184 1.32 - 1.44: 5116 1.44 - 1.57: 11017 1.57 - 1.69: 2 1.69 - 1.81: 144 Bond restraints: 19463 Sorted by residual: bond pdb=" C21 3PE A2311 " pdb=" O21 3PE A2311 " ideal model delta sigma weight residual 1.316 1.450 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C31 3PE A2311 " pdb=" O31 3PE A2311 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C THR F 362 " pdb=" O THR F 362 " ideal model delta sigma weight residual 1.234 1.200 0.034 1.22e-02 6.72e+03 7.84e+00 bond pdb=" C ASN F 184 " pdb=" N TRP F 185 " ideal model delta sigma weight residual 1.335 1.301 0.034 1.35e-02 5.49e+03 6.17e+00 bond pdb=" CA GLY F 365 " pdb=" C GLY F 365 " ideal model delta sigma weight residual 1.519 1.497 0.022 8.90e-03 1.26e+04 5.85e+00 ... (remaining 19458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 25749 1.86 - 3.72: 484 3.72 - 5.58: 56 5.58 - 7.44: 9 7.44 - 9.30: 3 Bond angle restraints: 26301 Sorted by residual: angle pdb=" CA PRO C 379 " pdb=" N PRO C 379 " pdb=" CD PRO C 379 " ideal model delta sigma weight residual 112.00 106.08 5.92 1.40e+00 5.10e-01 1.79e+01 angle pdb=" N VAL A 178 " pdb=" CA VAL A 178 " pdb=" C VAL A 178 " ideal model delta sigma weight residual 111.81 108.43 3.38 8.60e-01 1.35e+00 1.54e+01 angle pdb=" CA GLY F 365 " pdb=" C GLY F 365 " pdb=" O GLY F 365 " ideal model delta sigma weight residual 121.57 117.63 3.94 1.07e+00 8.73e-01 1.36e+01 angle pdb=" N ALA F 787 " pdb=" CA ALA F 787 " pdb=" CB ALA F 787 " ideal model delta sigma weight residual 114.17 110.07 4.10 1.14e+00 7.69e-01 1.29e+01 angle pdb=" C GLY F 364 " pdb=" N GLY F 365 " pdb=" CA GLY F 365 " ideal model delta sigma weight residual 121.82 118.85 2.97 8.40e-01 1.42e+00 1.25e+01 ... (remaining 26296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 10289 16.52 - 33.04: 1161 33.04 - 49.56: 222 49.56 - 66.09: 45 66.09 - 82.61: 12 Dihedral angle restraints: 11729 sinusoidal: 4891 harmonic: 6838 Sorted by residual: dihedral pdb=" CB CYS F 354 " pdb=" SG CYS F 354 " pdb=" SG CYS F1059 " pdb=" CB CYS F1059 " ideal model delta sinusoidal sigma weight residual -86.00 -10.73 -75.27 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual 93.00 136.35 -43.35 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CB CYS A1479 " pdb=" SG CYS A1479 " pdb=" SG CYS A1495 " pdb=" CB CYS A1495 " ideal model delta sinusoidal sigma weight residual -86.00 -48.53 -37.47 1 1.00e+01 1.00e-02 1.98e+01 ... (remaining 11726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2804 0.082 - 0.163: 173 0.163 - 0.245: 2 0.245 - 0.326: 0 0.326 - 0.408: 2 Chirality restraints: 2981 Sorted by residual: chirality pdb=" C1 NAG F1104 " pdb=" ND2 ASN F 184 " pdb=" C2 NAG F1104 " pdb=" O5 NAG F1104 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C1 NAG F1103 " pdb=" ND2 ASN F 92 " pdb=" C2 NAG F1103 " pdb=" O5 NAG F1103 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C1 NAG F1101 " pdb=" ND2 ASN F 468 " pdb=" C2 NAG F1101 " pdb=" O5 NAG F1101 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2978 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1103 " -0.287 2.00e-02 2.50e+03 2.52e-01 7.94e+02 pdb=" C7 NAG F1103 " 0.058 2.00e-02 2.50e+03 pdb=" C8 NAG F1103 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG F1103 " 0.445 2.00e-02 2.50e+03 pdb=" O7 NAG F1103 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1104 " -0.231 2.00e-02 2.50e+03 1.91e-01 4.58e+02 pdb=" C7 NAG F1104 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG F1104 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG F1104 " 0.313 2.00e-02 2.50e+03 pdb=" O7 NAG F1104 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1101 " 0.172 2.00e-02 2.50e+03 1.42e-01 2.52e+02 pdb=" C7 NAG F1101 " -0.047 2.00e-02 2.50e+03 pdb=" C8 NAG F1101 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG F1101 " -0.230 2.00e-02 2.50e+03 pdb=" O7 NAG F1101 " -0.022 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 197 2.55 - 3.14: 16961 3.14 - 3.73: 28978 3.73 - 4.31: 39951 4.31 - 4.90: 65531 Nonbonded interactions: 151618 Sorted by model distance: nonbonded pdb=" NH2 ARG F 240 " pdb=" OE1 GLU F 281 " model vdw 1.964 3.120 nonbonded pdb=" O ASP A1437 " pdb=" OG1 THR A1438 " model vdw 2.118 3.040 nonbonded pdb=" O GLY F 857 " pdb=" N PHE F 875 " model vdw 2.199 3.120 nonbonded pdb=" O TYR F 644 " pdb=" CG2 THR F 647 " model vdw 2.201 3.460 nonbonded pdb=" O LEU F 768 " pdb=" NZ LYS F 808 " model vdw 2.206 3.120 ... (remaining 151613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.590 Find NCS groups from input model: 0.090 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 0.134 19475 Z= 0.234 Angle : 0.634 9.299 26330 Z= 0.344 Chirality : 0.042 0.408 2981 Planarity : 0.008 0.252 3299 Dihedral : 14.178 82.607 7276 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.18), residues: 2292 helix: 0.72 (0.15), residues: 1137 sheet: -2.14 (0.36), residues: 210 loop : -1.84 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 240 TYR 0.012 0.001 TYR F 512 PHE 0.027 0.002 PHE F 780 TRP 0.010 0.001 TRP F 205 HIS 0.007 0.001 HIS A 545 Details of bonding type rmsd covalent geometry : bond 0.00490 (19463) covalent geometry : angle 0.62757 (26301) SS BOND : bond 0.00188 ( 7) SS BOND : angle 1.22079 ( 14) hydrogen bonds : bond 0.18950 ( 915) hydrogen bonds : angle 6.77738 ( 2670) link_NAG-ASN : bond 0.00658 ( 5) link_NAG-ASN : angle 3.71311 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.800 Fit side-chains REVERT: A 611 MET cc_start: 0.6171 (tmm) cc_final: 0.5888 (tmm) REVERT: A 936 PHE cc_start: 0.7683 (m-80) cc_final: 0.7186 (m-80) REVERT: A 1178 MET cc_start: 0.6642 (mmm) cc_final: 0.6374 (mmm) REVERT: A 1240 TYR cc_start: 0.7649 (m-10) cc_final: 0.7364 (m-80) REVERT: A 1615 ARG cc_start: 0.4771 (ptt180) cc_final: 0.4313 (ptt180) REVERT: F 198 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7597 (tm-30) REVERT: C 301 GLN cc_start: 0.7983 (mt0) cc_final: 0.7750 (mt0) REVERT: C 329 GLN cc_start: 0.6677 (mp10) cc_final: 0.6242 (mp10) REVERT: C 389 GLU cc_start: 0.6288 (pm20) cc_final: 0.6064 (pm20) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1241 time to fit residues: 64.0274 Evaluate side-chains 244 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN F 482 GLN F 641 GLN F 713 ASN F 888 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.143463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102450 restraints weight = 35927.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106109 restraints weight = 16711.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106502 restraints weight = 9483.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.106928 restraints weight = 9035.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107016 restraints weight = 8341.856| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19475 Z= 0.156 Angle : 0.625 12.587 26330 Z= 0.323 Chirality : 0.044 0.265 2981 Planarity : 0.005 0.093 3299 Dihedral : 7.427 68.566 2779 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.16 % Allowed : 8.50 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.18), residues: 2292 helix: 0.69 (0.15), residues: 1206 sheet: -1.93 (0.36), residues: 210 loop : -1.72 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 240 TYR 0.025 0.002 TYR A1222 PHE 0.025 0.002 PHE C 258 TRP 0.014 0.001 TRP F 185 HIS 0.006 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00343 (19463) covalent geometry : angle 0.62272 (26301) SS BOND : bond 0.00528 ( 7) SS BOND : angle 1.30005 ( 14) hydrogen bonds : bond 0.05041 ( 915) hydrogen bonds : angle 5.12499 ( 2670) link_NAG-ASN : bond 0.00685 ( 5) link_NAG-ASN : angle 1.75755 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 0.817 Fit side-chains REVERT: A 634 TRP cc_start: 0.5881 (m-90) cc_final: 0.5562 (m-90) REVERT: A 936 PHE cc_start: 0.7977 (m-80) cc_final: 0.7472 (m-80) REVERT: A 1119 ASP cc_start: 0.8264 (m-30) cc_final: 0.8044 (m-30) REVERT: A 1125 MET cc_start: 0.8037 (mtp) cc_final: 0.7813 (mtp) REVERT: A 1240 TYR cc_start: 0.7597 (m-10) cc_final: 0.7301 (m-80) REVERT: A 1271 MET cc_start: 0.8787 (mmt) cc_final: 0.8551 (mmp) REVERT: F 198 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7668 (tm-30) REVERT: F 233 ILE cc_start: 0.8746 (mp) cc_final: 0.8505 (mp) REVERT: C 227 MET cc_start: 0.3973 (mmm) cc_final: 0.1837 (tpt) REVERT: C 305 GLU cc_start: 0.8947 (pp20) cc_final: 0.8544 (pt0) REVERT: C 329 GLN cc_start: 0.6308 (mp10) cc_final: 0.6063 (mp10) REVERT: C 351 GLN cc_start: 0.8957 (mp10) cc_final: 0.8656 (mp10) REVERT: C 368 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8387 (tp40) outliers start: 24 outliers final: 14 residues processed: 301 average time/residue: 0.1331 time to fit residues: 65.3694 Evaluate side-chains 267 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 671 LYS Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 170 optimal weight: 0.0980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 HIS ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 GLN A1445 ASN F 392 HIS F 443 GLN C 301 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.144287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102473 restraints weight = 36213.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106932 restraints weight = 17026.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107442 restraints weight = 9333.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107644 restraints weight = 8532.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107750 restraints weight = 8128.724| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19475 Z= 0.139 Angle : 0.595 12.032 26330 Z= 0.302 Chirality : 0.043 0.244 2981 Planarity : 0.004 0.074 3299 Dihedral : 7.245 59.276 2779 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.88 % Allowed : 12.90 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.18), residues: 2292 helix: 0.68 (0.15), residues: 1216 sheet: -1.80 (0.36), residues: 209 loop : -1.68 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 257 TYR 0.018 0.001 TYR F 512 PHE 0.028 0.001 PHE A1004 TRP 0.017 0.001 TRP F 185 HIS 0.004 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00309 (19463) covalent geometry : angle 0.59377 (26301) SS BOND : bond 0.00233 ( 7) SS BOND : angle 0.97999 ( 14) hydrogen bonds : bond 0.04171 ( 915) hydrogen bonds : angle 4.79693 ( 2670) link_NAG-ASN : bond 0.00379 ( 5) link_NAG-ASN : angle 1.28187 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 299 time to evaluate : 0.797 Fit side-chains REVERT: A 200 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6914 (t80) REVERT: A 433 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7746 (t0) REVERT: A 602 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7505 (mt-10) REVERT: A 936 PHE cc_start: 0.7996 (m-80) cc_final: 0.7515 (m-80) REVERT: A 1119 ASP cc_start: 0.8316 (m-30) cc_final: 0.8099 (m-30) REVERT: A 1125 MET cc_start: 0.8132 (mtp) cc_final: 0.7833 (mtp) REVERT: A 1222 TYR cc_start: 0.7271 (t80) cc_final: 0.6874 (t80) REVERT: A 1240 TYR cc_start: 0.7515 (m-10) cc_final: 0.7137 (m-80) REVERT: A 1271 MET cc_start: 0.8726 (mmt) cc_final: 0.8494 (mmp) REVERT: A 1272 ASN cc_start: 0.7961 (m-40) cc_final: 0.7708 (m-40) REVERT: F 233 ILE cc_start: 0.8728 (mp) cc_final: 0.8464 (mp) REVERT: F 278 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7718 (mm-30) REVERT: F 801 TYR cc_start: 0.7895 (m-80) cc_final: 0.7582 (m-80) REVERT: F 878 ILE cc_start: 0.7778 (mm) cc_final: 0.7567 (mm) REVERT: C 227 MET cc_start: 0.3892 (mmm) cc_final: 0.1755 (tpt) REVERT: C 244 ASP cc_start: 0.7430 (t70) cc_final: 0.7108 (t0) REVERT: C 305 GLU cc_start: 0.8945 (pp20) cc_final: 0.8575 (pt0) REVERT: C 329 GLN cc_start: 0.6206 (mp10) cc_final: 0.5926 (mp10) REVERT: C 368 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8410 (tp40) REVERT: C 398 HIS cc_start: 0.6410 (t70) cc_final: 0.5997 (t70) outliers start: 39 outliers final: 22 residues processed: 322 average time/residue: 0.1370 time to fit residues: 71.4058 Evaluate side-chains 293 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 269 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 864 HIS Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 15 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 228 optimal weight: 0.0270 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN A 987 ASN A1445 ASN F 641 GLN C 301 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.145972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103568 restraints weight = 36933.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107427 restraints weight = 17756.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107807 restraints weight = 10238.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108329 restraints weight = 9787.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108293 restraints weight = 8828.597| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19475 Z= 0.121 Angle : 0.582 12.940 26330 Z= 0.293 Chirality : 0.042 0.286 2981 Planarity : 0.004 0.066 3299 Dihedral : 7.071 59.132 2779 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.13 % Allowed : 14.98 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.18), residues: 2292 helix: 0.79 (0.15), residues: 1211 sheet: -1.61 (0.35), residues: 219 loop : -1.57 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 257 TYR 0.015 0.001 TYR F 512 PHE 0.024 0.001 PHE A1004 TRP 0.016 0.001 TRP F 185 HIS 0.007 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00264 (19463) covalent geometry : angle 0.58099 (26301) SS BOND : bond 0.00226 ( 7) SS BOND : angle 0.81352 ( 14) hydrogen bonds : bond 0.03827 ( 915) hydrogen bonds : angle 4.62319 ( 2670) link_NAG-ASN : bond 0.00340 ( 5) link_NAG-ASN : angle 1.20068 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 0.734 Fit side-chains REVERT: A 236 LEU cc_start: 0.8753 (tp) cc_final: 0.8110 (tt) REVERT: A 433 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7699 (t0) REVERT: A 602 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7523 (mt-10) REVERT: A 762 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7683 (tp) REVERT: A 766 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: A 936 PHE cc_start: 0.8074 (m-80) cc_final: 0.7618 (m-80) REVERT: A 1125 MET cc_start: 0.8148 (mtp) cc_final: 0.7863 (mtp) REVERT: A 1222 TYR cc_start: 0.7321 (t80) cc_final: 0.6716 (t80) REVERT: A 1240 TYR cc_start: 0.7489 (m-10) cc_final: 0.7062 (m-80) REVERT: A 1272 ASN cc_start: 0.8083 (m-40) cc_final: 0.7809 (m-40) REVERT: A 1526 ASN cc_start: 0.8039 (t0) cc_final: 0.7681 (t0) REVERT: F 233 ILE cc_start: 0.8753 (mp) cc_final: 0.8504 (mp) REVERT: F 278 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7791 (mm-30) REVERT: F 594 SER cc_start: 0.8919 (t) cc_final: 0.8514 (p) REVERT: F 801 TYR cc_start: 0.7920 (m-80) cc_final: 0.7620 (m-80) REVERT: C 227 MET cc_start: 0.3674 (mmm) cc_final: 0.1574 (tpt) REVERT: C 244 ASP cc_start: 0.7415 (t70) cc_final: 0.7172 (t0) REVERT: C 329 GLN cc_start: 0.6191 (mp10) cc_final: 0.5922 (mp10) REVERT: C 351 GLN cc_start: 0.8916 (mp10) cc_final: 0.8683 (mp10) REVERT: C 368 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8512 (tp40) outliers start: 44 outliers final: 19 residues processed: 323 average time/residue: 0.1242 time to fit residues: 65.4717 Evaluate side-chains 296 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 274 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 864 HIS Chi-restraints excluded: chain F residue 994 LEU Chi-restraints excluded: chain F residue 1016 ILE Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 147 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 158 optimal weight: 0.0010 chunk 99 optimal weight: 0.0470 chunk 204 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN C 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.147188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105390 restraints weight = 36919.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108442 restraints weight = 17955.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110046 restraints weight = 10540.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110089 restraints weight = 9642.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110002 restraints weight = 8576.897| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 19475 Z= 0.117 Angle : 0.585 13.469 26330 Z= 0.293 Chirality : 0.042 0.349 2981 Planarity : 0.004 0.062 3299 Dihedral : 6.911 58.897 2779 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.74 % Allowed : 16.33 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2292 helix: 0.89 (0.15), residues: 1211 sheet: -1.54 (0.35), residues: 220 loop : -1.49 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 257 TYR 0.014 0.001 TYR F 512 PHE 0.026 0.001 PHE A1611 TRP 0.015 0.001 TRP F 821 HIS 0.005 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00248 (19463) covalent geometry : angle 0.58416 (26301) SS BOND : bond 0.00202 ( 7) SS BOND : angle 0.71649 ( 14) hydrogen bonds : bond 0.03648 ( 915) hydrogen bonds : angle 4.50607 ( 2670) link_NAG-ASN : bond 0.00425 ( 5) link_NAG-ASN : angle 1.18958 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 0.822 Fit side-chains REVERT: A 200 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 236 LEU cc_start: 0.8444 (tp) cc_final: 0.8050 (tt) REVERT: A 433 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7637 (t0) REVERT: A 439 ASP cc_start: 0.8588 (t0) cc_final: 0.8359 (t70) REVERT: A 602 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7555 (mt-10) REVERT: A 936 PHE cc_start: 0.8132 (m-80) cc_final: 0.7652 (m-80) REVERT: A 1069 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7967 (mm110) REVERT: A 1117 ASP cc_start: 0.7578 (p0) cc_final: 0.6953 (p0) REVERT: A 1125 MET cc_start: 0.8102 (mtp) cc_final: 0.7820 (mtp) REVERT: A 1222 TYR cc_start: 0.7437 (t80) cc_final: 0.6785 (t80) REVERT: A 1240 TYR cc_start: 0.7418 (m-10) cc_final: 0.6993 (m-80) REVERT: A 1272 ASN cc_start: 0.8065 (m-40) cc_final: 0.7788 (m-40) REVERT: A 1526 ASN cc_start: 0.8031 (t0) cc_final: 0.7606 (t0) REVERT: F 233 ILE cc_start: 0.8783 (mp) cc_final: 0.8545 (mp) REVERT: F 278 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7667 (mm-30) REVERT: F 279 MET cc_start: 0.8393 (tpp) cc_final: 0.7745 (ttm) REVERT: F 594 SER cc_start: 0.8908 (t) cc_final: 0.8532 (p) REVERT: F 646 GLU cc_start: 0.8308 (pm20) cc_final: 0.8038 (pm20) REVERT: F 744 TYR cc_start: 0.7022 (t80) cc_final: 0.6707 (t80) REVERT: F 801 TYR cc_start: 0.7951 (m-80) cc_final: 0.7720 (m-80) REVERT: C 227 MET cc_start: 0.3621 (mmm) cc_final: 0.1632 (tpt) REVERT: C 305 GLU cc_start: 0.8879 (pp20) cc_final: 0.8637 (pt0) REVERT: C 329 GLN cc_start: 0.6043 (mp10) cc_final: 0.5775 (mp10) REVERT: C 351 GLN cc_start: 0.8836 (mp10) cc_final: 0.8580 (mp10) REVERT: C 368 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8531 (tp40) outliers start: 36 outliers final: 22 residues processed: 327 average time/residue: 0.1267 time to fit residues: 66.9501 Evaluate side-chains 301 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 277 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 864 HIS Chi-restraints excluded: chain F residue 994 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 165 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 109 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 ASN C 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.146951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104736 restraints weight = 36865.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108742 restraints weight = 17731.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109083 restraints weight = 10052.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109684 restraints weight = 9646.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109575 restraints weight = 8713.361| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19475 Z= 0.118 Angle : 0.581 13.731 26330 Z= 0.290 Chirality : 0.042 0.318 2981 Planarity : 0.004 0.060 3299 Dihedral : 6.810 59.037 2779 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.98 % Allowed : 17.25 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.18), residues: 2292 helix: 0.97 (0.15), residues: 1207 sheet: -1.48 (0.35), residues: 220 loop : -1.43 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 257 TYR 0.014 0.001 TYR F 719 PHE 0.026 0.001 PHE A 594 TRP 0.017 0.001 TRP F 821 HIS 0.008 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00262 (19463) covalent geometry : angle 0.58021 (26301) SS BOND : bond 0.00224 ( 7) SS BOND : angle 0.72139 ( 14) hydrogen bonds : bond 0.03528 ( 915) hydrogen bonds : angle 4.43101 ( 2670) link_NAG-ASN : bond 0.00323 ( 5) link_NAG-ASN : angle 1.17260 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 298 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7209 (tm-30) REVERT: A 200 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6845 (t80) REVERT: A 236 LEU cc_start: 0.8402 (tp) cc_final: 0.8062 (tt) REVERT: A 433 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7638 (t0) REVERT: A 439 ASP cc_start: 0.8616 (t0) cc_final: 0.8392 (t70) REVERT: A 602 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7453 (mt-10) REVERT: A 909 PHE cc_start: 0.8101 (m-80) cc_final: 0.7755 (m-80) REVERT: A 936 PHE cc_start: 0.8135 (m-80) cc_final: 0.7680 (m-80) REVERT: A 1029 ILE cc_start: 0.8772 (mt) cc_final: 0.8524 (mp) REVERT: A 1125 MET cc_start: 0.8111 (mtp) cc_final: 0.7829 (mtp) REVERT: A 1222 TYR cc_start: 0.7498 (t80) cc_final: 0.6847 (t80) REVERT: A 1240 TYR cc_start: 0.7455 (m-10) cc_final: 0.7023 (m-80) REVERT: A 1258 MET cc_start: 0.7786 (ttm) cc_final: 0.7332 (ttm) REVERT: A 1272 ASN cc_start: 0.8019 (m-40) cc_final: 0.7786 (m110) REVERT: A 1526 ASN cc_start: 0.8173 (t0) cc_final: 0.7719 (t0) REVERT: A 1611 PHE cc_start: 0.7865 (t80) cc_final: 0.7541 (t80) REVERT: F 233 ILE cc_start: 0.8771 (mp) cc_final: 0.8527 (mp) REVERT: F 278 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7656 (mm-30) REVERT: F 279 MET cc_start: 0.8228 (tpp) cc_final: 0.7795 (ttm) REVERT: F 359 MET cc_start: 0.8151 (mtp) cc_final: 0.7745 (mtp) REVERT: F 594 SER cc_start: 0.8930 (t) cc_final: 0.8546 (p) REVERT: F 646 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: F 744 TYR cc_start: 0.7030 (t80) cc_final: 0.6781 (t80) REVERT: F 1035 GLU cc_start: 0.8578 (pp20) cc_final: 0.8288 (pp20) REVERT: C 227 MET cc_start: 0.3653 (mmm) cc_final: 0.1710 (tpt) REVERT: C 351 GLN cc_start: 0.8801 (mp10) cc_final: 0.8534 (mp10) outliers start: 41 outliers final: 28 residues processed: 320 average time/residue: 0.1384 time to fit residues: 71.5450 Evaluate side-chains 310 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 646 GLU Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 864 HIS Chi-restraints excluded: chain F residue 875 PHE Chi-restraints excluded: chain F residue 994 LEU Chi-restraints excluded: chain F residue 1016 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 12 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 129 optimal weight: 0.0470 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN A 766 GLN ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 GLN F 668 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.146273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.104313 restraints weight = 36745.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107033 restraints weight = 18252.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108172 restraints weight = 10886.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108539 restraints weight = 9830.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108703 restraints weight = 8898.960| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19475 Z= 0.130 Angle : 0.593 14.022 26330 Z= 0.296 Chirality : 0.042 0.242 2981 Planarity : 0.004 0.058 3299 Dihedral : 6.790 59.454 2779 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.46 % Allowed : 18.02 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.18), residues: 2292 helix: 0.97 (0.15), residues: 1211 sheet: -1.45 (0.35), residues: 220 loop : -1.43 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 257 TYR 0.014 0.001 TYR F 512 PHE 0.031 0.001 PHE A1507 TRP 0.021 0.001 TRP F 821 HIS 0.006 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00297 (19463) covalent geometry : angle 0.59280 (26301) SS BOND : bond 0.00223 ( 7) SS BOND : angle 0.79471 ( 14) hydrogen bonds : bond 0.03523 ( 915) hydrogen bonds : angle 4.41400 ( 2670) link_NAG-ASN : bond 0.00288 ( 5) link_NAG-ASN : angle 1.16333 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 284 time to evaluate : 0.833 Fit side-chains REVERT: A 200 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6908 (t80) REVERT: A 236 LEU cc_start: 0.8439 (tp) cc_final: 0.8201 (tt) REVERT: A 239 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8342 (t80) REVERT: A 291 MET cc_start: 0.7506 (tpt) cc_final: 0.7045 (tpp) REVERT: A 433 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7672 (t0) REVERT: A 439 ASP cc_start: 0.8604 (t0) cc_final: 0.8375 (t70) REVERT: A 588 PHE cc_start: 0.8036 (t80) cc_final: 0.7704 (t80) REVERT: A 602 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7625 (mt-10) REVERT: A 931 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7235 (t70) REVERT: A 936 PHE cc_start: 0.8186 (m-80) cc_final: 0.7737 (m-80) REVERT: A 1029 ILE cc_start: 0.8773 (mt) cc_final: 0.8520 (mp) REVERT: A 1069 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7887 (mm110) REVERT: A 1125 MET cc_start: 0.8118 (mtp) cc_final: 0.7828 (mtp) REVERT: A 1222 TYR cc_start: 0.7552 (t80) cc_final: 0.6897 (t80) REVERT: A 1240 TYR cc_start: 0.7391 (m-10) cc_final: 0.6972 (m-80) REVERT: A 1258 MET cc_start: 0.7775 (ttm) cc_final: 0.7320 (ttm) REVERT: A 1272 ASN cc_start: 0.8011 (m-40) cc_final: 0.7776 (m-40) REVERT: A 1526 ASN cc_start: 0.8281 (t0) cc_final: 0.7801 (t0) REVERT: F 233 ILE cc_start: 0.8747 (mp) cc_final: 0.8460 (mp) REVERT: F 279 MET cc_start: 0.8363 (tpp) cc_final: 0.7872 (ttm) REVERT: F 359 MET cc_start: 0.7924 (mtp) cc_final: 0.7707 (mtp) REVERT: F 594 SER cc_start: 0.8921 (t) cc_final: 0.8527 (p) REVERT: F 744 TYR cc_start: 0.7052 (t80) cc_final: 0.6839 (t80) REVERT: F 861 MET cc_start: 0.7485 (mmm) cc_final: 0.7061 (mtp) REVERT: C 227 MET cc_start: 0.3788 (mmm) cc_final: 0.1836 (tpt) REVERT: C 351 GLN cc_start: 0.8778 (mp10) cc_final: 0.8496 (mp10) REVERT: C 369 MET cc_start: 0.9076 (ppp) cc_final: 0.8871 (ppp) outliers start: 51 outliers final: 36 residues processed: 313 average time/residue: 0.1334 time to fit residues: 67.0910 Evaluate side-chains 314 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 668 ASN Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 864 HIS Chi-restraints excluded: chain F residue 875 PHE Chi-restraints excluded: chain F residue 883 MET Chi-restraints excluded: chain F residue 994 LEU Chi-restraints excluded: chain F residue 1016 ILE Chi-restraints excluded: chain F residue 1071 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 48 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 220 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 ASN ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.147477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105610 restraints weight = 36735.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108276 restraints weight = 18467.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108737 restraints weight = 11063.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109172 restraints weight = 10933.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109258 restraints weight = 9930.138| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19475 Z= 0.115 Angle : 0.593 14.566 26330 Z= 0.295 Chirality : 0.042 0.241 2981 Planarity : 0.004 0.057 3299 Dihedral : 6.702 59.473 2779 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.13 % Allowed : 18.16 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.18), residues: 2292 helix: 1.05 (0.15), residues: 1210 sheet: -1.38 (0.36), residues: 219 loop : -1.38 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 257 TYR 0.015 0.001 TYR F 719 PHE 0.035 0.001 PHE A1507 TRP 0.023 0.001 TRP F 821 HIS 0.005 0.000 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00254 (19463) covalent geometry : angle 0.59264 (26301) SS BOND : bond 0.00192 ( 7) SS BOND : angle 0.71952 ( 14) hydrogen bonds : bond 0.03409 ( 915) hydrogen bonds : angle 4.36361 ( 2670) link_NAG-ASN : bond 0.00321 ( 5) link_NAG-ASN : angle 1.14727 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 0.716 Fit side-chains REVERT: A 200 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6959 (t80) REVERT: A 236 LEU cc_start: 0.8409 (tp) cc_final: 0.8192 (tt) REVERT: A 239 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8322 (t80) REVERT: A 291 MET cc_start: 0.7389 (tpt) cc_final: 0.6970 (tpp) REVERT: A 433 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7671 (t0) REVERT: A 439 ASP cc_start: 0.8585 (t0) cc_final: 0.8357 (t70) REVERT: A 707 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7413 (t0) REVERT: A 746 ASN cc_start: 0.8761 (t0) cc_final: 0.8487 (t0) REVERT: A 909 PHE cc_start: 0.7972 (m-80) cc_final: 0.7738 (m-80) REVERT: A 931 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7274 (t70) REVERT: A 936 PHE cc_start: 0.8266 (m-80) cc_final: 0.7814 (m-80) REVERT: A 1029 ILE cc_start: 0.8761 (mt) cc_final: 0.8502 (mp) REVERT: A 1125 MET cc_start: 0.8076 (mtp) cc_final: 0.7808 (mtp) REVERT: A 1191 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6856 (tm-30) REVERT: A 1222 TYR cc_start: 0.7568 (t80) cc_final: 0.6932 (t80) REVERT: A 1240 TYR cc_start: 0.7369 (m-10) cc_final: 0.6904 (m-80) REVERT: A 1258 MET cc_start: 0.7785 (ttm) cc_final: 0.7316 (ttm) REVERT: A 1272 ASN cc_start: 0.8005 (m-40) cc_final: 0.7777 (m-40) REVERT: A 1286 MET cc_start: 0.8961 (tpt) cc_final: 0.8745 (tpt) REVERT: A 1526 ASN cc_start: 0.8313 (t0) cc_final: 0.7757 (t0) REVERT: F 233 ILE cc_start: 0.8775 (mp) cc_final: 0.8502 (mp) REVERT: F 279 MET cc_start: 0.8374 (tpp) cc_final: 0.7892 (ttm) REVERT: F 594 SER cc_start: 0.8927 (t) cc_final: 0.8583 (p) REVERT: C 227 MET cc_start: 0.3780 (mmm) cc_final: 0.1769 (tpt) REVERT: C 351 GLN cc_start: 0.8847 (mp10) cc_final: 0.8624 (mp10) outliers start: 44 outliers final: 33 residues processed: 311 average time/residue: 0.1361 time to fit residues: 68.0885 Evaluate side-chains 308 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 864 HIS Chi-restraints excluded: chain F residue 875 PHE Chi-restraints excluded: chain F residue 994 LEU Chi-restraints excluded: chain F residue 1071 CYS Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 150 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 44 optimal weight: 0.0000 chunk 51 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** 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 = 0.3938 r_free = 0.3938 target = 0.141533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097055 restraints weight = 36756.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.100105 restraints weight = 17461.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.102111 restraints weight = 11440.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103140 restraints weight = 8945.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.103861 restraints weight = 7855.277| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 19475 Z= 0.287 Angle : 0.727 13.730 26330 Z= 0.368 Chirality : 0.047 0.259 2981 Planarity : 0.005 0.056 3299 Dihedral : 7.386 58.233 2779 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.13 % Allowed : 19.13 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.18), residues: 2292 helix: 0.67 (0.14), residues: 1214 sheet: -1.64 (0.37), residues: 210 loop : -1.60 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 499 TYR 0.020 0.002 TYR F 744 PHE 0.042 0.002 PHE A1507 TRP 0.027 0.002 TRP F 821 HIS 0.004 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00664 (19463) covalent geometry : angle 0.72528 (26301) SS BOND : bond 0.00443 ( 7) SS BOND : angle 1.46705 ( 14) hydrogen bonds : bond 0.04218 ( 915) hydrogen bonds : angle 4.74512 ( 2670) link_NAG-ASN : bond 0.00390 ( 5) link_NAG-ASN : angle 1.62816 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 0.782 Fit side-chains REVERT: A 200 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6553 (t80) REVERT: A 236 LEU cc_start: 0.8665 (tp) cc_final: 0.8024 (tp) REVERT: A 433 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7861 (t0) REVERT: A 707 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7641 (t70) REVERT: A 931 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7271 (t70) REVERT: A 936 PHE cc_start: 0.8121 (m-80) cc_final: 0.7696 (m-80) REVERT: A 1069 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7854 (mm110) REVERT: A 1117 ASP cc_start: 0.7592 (p0) cc_final: 0.7051 (p0) REVERT: A 1125 MET cc_start: 0.8195 (mtp) cc_final: 0.7883 (mtp) REVERT: A 1222 TYR cc_start: 0.7507 (t80) cc_final: 0.6915 (t80) REVERT: A 1240 TYR cc_start: 0.7296 (m-10) cc_final: 0.6909 (m-80) REVERT: A 1258 MET cc_start: 0.7997 (ttm) cc_final: 0.7600 (ttm) REVERT: A 1526 ASN cc_start: 0.8237 (t0) cc_final: 0.7188 (t0) REVERT: F 171 ASP cc_start: 0.8350 (p0) cc_final: 0.8108 (p0) REVERT: F 233 ILE cc_start: 0.8804 (mp) cc_final: 0.8463 (mp) REVERT: F 279 MET cc_start: 0.8766 (tpp) cc_final: 0.8071 (ttp) REVERT: C 227 MET cc_start: 0.3624 (mmm) cc_final: 0.1684 (tpt) REVERT: C 369 MET cc_start: 0.9131 (ppp) cc_final: 0.8859 (ppp) outliers start: 44 outliers final: 37 residues processed: 288 average time/residue: 0.1354 time to fit residues: 63.5156 Evaluate side-chains 293 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 1004 PHE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 864 HIS Chi-restraints excluded: chain F residue 875 PHE Chi-restraints excluded: chain F residue 883 MET Chi-restraints excluded: chain F residue 1071 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 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 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.145245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102714 restraints weight = 36432.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105930 restraints weight = 17586.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106892 restraints weight = 10476.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107252 restraints weight = 9704.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107112 restraints weight = 8675.403| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 0.040 19475 Z= 0.134 Angle : 0.634 15.716 26330 Z= 0.315 Chirality : 0.043 0.234 2981 Planarity : 0.004 0.058 3299 Dihedral : 7.006 58.153 2779 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.64 % Allowed : 20.05 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2292 helix: 0.85 (0.15), residues: 1220 sheet: -1.53 (0.35), residues: 222 loop : -1.46 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 643 TYR 0.016 0.001 TYR F 512 PHE 0.035 0.001 PHE A1507 TRP 0.027 0.001 TRP F 821 HIS 0.005 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00307 (19463) covalent geometry : angle 0.63325 (26301) SS BOND : bond 0.00226 ( 7) SS BOND : angle 0.90749 ( 14) hydrogen bonds : bond 0.03634 ( 915) hydrogen bonds : angle 4.54732 ( 2670) link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 1.23338 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.964 Fit side-chains REVERT: A 200 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6595 (t80) REVERT: A 236 LEU cc_start: 0.8455 (tp) cc_final: 0.8006 (tt) REVERT: A 433 ASP cc_start: 0.8088 (m-30) cc_final: 0.7719 (t0) REVERT: A 588 PHE cc_start: 0.7946 (t80) cc_final: 0.7488 (t80) REVERT: A 707 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7551 (t0) REVERT: A 931 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7378 (t70) REVERT: A 936 PHE cc_start: 0.8202 (m-80) cc_final: 0.7755 (m-80) REVERT: A 1029 ILE cc_start: 0.8708 (mt) cc_final: 0.8459 (mp) REVERT: A 1069 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7816 (mm110) REVERT: A 1117 ASP cc_start: 0.7368 (p0) cc_final: 0.6912 (p0) REVERT: A 1222 TYR cc_start: 0.7627 (t80) cc_final: 0.7007 (t80) REVERT: A 1240 TYR cc_start: 0.7287 (m-10) cc_final: 0.6819 (m-80) REVERT: A 1258 MET cc_start: 0.7938 (ttm) cc_final: 0.7503 (ttm) REVERT: A 1286 MET cc_start: 0.8953 (tpt) cc_final: 0.8751 (tpt) REVERT: A 1526 ASN cc_start: 0.8160 (t0) cc_final: 0.7649 (t0) REVERT: F 233 ILE cc_start: 0.8820 (mp) cc_final: 0.8519 (mp) REVERT: F 278 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7658 (mm-30) REVERT: F 279 MET cc_start: 0.8408 (tpp) cc_final: 0.8001 (ttp) REVERT: F 359 MET cc_start: 0.8077 (mtp) cc_final: 0.7750 (mtp) REVERT: F 896 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8786 (ttmm) REVERT: C 227 MET cc_start: 0.3745 (mmm) cc_final: 0.1766 (tpt) REVERT: C 329 GLN cc_start: 0.7108 (mp10) cc_final: 0.6887 (mp10) outliers start: 34 outliers final: 27 residues processed: 284 average time/residue: 0.1379 time to fit residues: 63.1564 Evaluate side-chains 287 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 931 HIS Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 640 THR Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 864 HIS Chi-restraints excluded: chain F residue 883 MET Chi-restraints excluded: chain F residue 1071 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 341 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 0.1980 chunk 198 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 196 optimal weight: 0.4980 chunk 123 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 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 746 ASN A1060 GLN A1445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.146832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104491 restraints weight = 36751.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.107771 restraints weight = 17464.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108373 restraints weight = 10353.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108915 restraints weight = 9931.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108878 restraints weight = 8846.525| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19475 Z= 0.120 Angle : 0.612 14.932 26330 Z= 0.305 Chirality : 0.042 0.235 2981 Planarity : 0.004 0.068 3299 Dihedral : 6.770 57.399 2779 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.64 % Allowed : 20.00 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.18), residues: 2292 helix: 0.98 (0.15), residues: 1216 sheet: -1.48 (0.35), residues: 222 loop : -1.43 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 643 TYR 0.018 0.001 TYR A 583 PHE 0.032 0.001 PHE F 780 TRP 0.027 0.001 TRP F 821 HIS 0.013 0.001 HIS A1148 Details of bonding type rmsd covalent geometry : bond 0.00269 (19463) covalent geometry : angle 0.61161 (26301) SS BOND : bond 0.00209 ( 7) SS BOND : angle 0.77698 ( 14) hydrogen bonds : bond 0.03436 ( 915) hydrogen bonds : angle 4.45273 ( 2670) link_NAG-ASN : bond 0.00324 ( 5) link_NAG-ASN : angle 1.11694 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3761.12 seconds wall clock time: 65 minutes 48.34 seconds (3948.34 seconds total)