Starting phenix.real_space_refine on Mon Jun 16 22:37:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hlp_34880/06_2025/8hlp_34880.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hlp_34880/06_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_34880/06_2025/8hlp_34880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hlp_34880/06_2025/8hlp_34880.map" model { file = "/net/cci-nas-00/data/ceres_data/8hlp_34880/06_2025/8hlp_34880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hlp_34880/06_2025/8hlp_34880.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.64, per 1000 atoms: 0.56 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: 4.67 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.88 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: 10.26 Time building geometry restraints manager: 5.45 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: 2.150 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: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 47.870 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.090 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.550 ------------------------------------------------------------------------------- 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 : 10.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), 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 TRP 0.010 0.001 TRP F 205 HIS 0.007 0.001 HIS A 545 PHE 0.027 0.002 PHE F 780 TYR 0.012 0.001 TYR F 512 ARG 0.005 0.000 ARG F 240 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 5) link_NAG-ASN : angle 3.71311 ( 15) hydrogen bonds : bond 0.18950 ( 915) hydrogen bonds : angle 6.77738 ( 2670) SS BOND : bond 0.00188 ( 7) SS BOND : angle 1.22079 ( 14) covalent geometry : bond 0.00490 (19463) covalent geometry : angle 0.62757 (26301) *********************** 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 : 2.822 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: 0.7747 (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: 0.2532 time to fit residues: 129.7311 Evaluate side-chains 245 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 210 optimal weight: 0.0470 overall best weight: 1.1082 ------------------------------------------------------------------------------- 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 ** A1120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 641 GLN F 713 ASN F 888 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.143523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102575 restraints weight = 35804.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105812 restraints weight = 16579.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107215 restraints weight = 9698.733| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1274 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= 0.158 Angle : 0.632 12.704 26330 Z= 0.326 Chirality : 0.044 0.248 2981 Planarity : 0.005 0.093 3299 Dihedral : 7.426 68.391 2779 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.21 % Allowed : 8.50 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2292 helix: 0.69 (0.15), residues: 1206 sheet: -1.82 (0.35), residues: 220 loop : -1.72 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 185 HIS 0.006 0.001 HIS A1148 PHE 0.026 0.002 PHE A 661 TYR 0.025 0.001 TYR A1222 ARG 0.006 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 5) link_NAG-ASN : angle 1.71750 ( 15) hydrogen bonds : bond 0.04913 ( 915) hydrogen bonds : angle 5.11715 ( 2670) SS BOND : bond 0.00946 ( 7) SS BOND : angle 1.25849 ( 14) covalent geometry : bond 0.00348 (19463) covalent geometry : angle 0.63057 (26301) *********************** 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 313 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 288 time to evaluate : 2.151 Fit side-chains REVERT: A 634 TRP cc_start: 0.5870 (m-90) cc_final: 0.5583 (m-90) REVERT: A 936 PHE cc_start: 0.7966 (m-80) cc_final: 0.7509 (m-80) REVERT: A 1119 ASP cc_start: 0.8262 (m-30) cc_final: 0.8032 (m-30) REVERT: A 1125 MET cc_start: 0.8032 (mtp) cc_final: 0.7811 (mtp) REVERT: A 1240 TYR cc_start: 0.7577 (m-10) cc_final: 0.7291 (m-80) REVERT: A 1271 MET cc_start: 0.8776 (mmt) cc_final: 0.8539 (mmp) REVERT: F 233 ILE cc_start: 0.8740 (mp) cc_final: 0.8498 (mp) REVERT: F 704 ARG cc_start: 0.8366 (ttp-170) cc_final: 0.7731 (ttp-170) REVERT: C 227 MET cc_start: 0.3968 (mmm) cc_final: 0.1822 (tpt) REVERT: C 305 GLU cc_start: 0.8927 (pp20) cc_final: 0.8517 (pt0) REVERT: C 329 GLN cc_start: 0.6215 (mp10) cc_final: 0.5956 (mp10) REVERT: C 351 GLN cc_start: 0.8951 (mp10) cc_final: 0.8641 (mp10) REVERT: C 368 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8383 (tp40) outliers start: 25 outliers final: 14 residues processed: 302 average time/residue: 0.2885 time to fit residues: 143.7213 Evaluate side-chains 269 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 255 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 105 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 186 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 GLN A1445 ASN F 392 HIS F 443 GLN ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.144343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102577 restraints weight = 35900.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.106807 restraints weight = 16918.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107690 restraints weight = 9375.712| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19475 Z= 0.137 Angle : 0.591 12.063 26330 Z= 0.301 Chirality : 0.043 0.248 2981 Planarity : 0.004 0.074 3299 Dihedral : 7.239 58.904 2779 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.88 % Allowed : 12.85 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2292 helix: 0.69 (0.15), residues: 1216 sheet: -1.79 (0.36), residues: 209 loop : -1.67 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 185 HIS 0.006 0.001 HIS A1148 PHE 0.028 0.001 PHE A1004 TYR 0.018 0.001 TYR F 512 ARG 0.004 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00332 ( 5) link_NAG-ASN : angle 1.24825 ( 15) hydrogen bonds : bond 0.04168 ( 915) hydrogen bonds : angle 4.77817 ( 2670) SS BOND : bond 0.00264 ( 7) SS BOND : angle 0.97585 ( 14) covalent geometry : bond 0.00304 (19463) covalent geometry : angle 0.59047 (26301) *********************** 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 339 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 300 time to evaluate : 2.235 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6938 (t80) REVERT: A 433 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7741 (t0) REVERT: A 602 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7473 (mt-10) REVERT: A 936 PHE cc_start: 0.7992 (m-80) cc_final: 0.7512 (m-80) REVERT: A 1119 ASP cc_start: 0.8285 (m-30) cc_final: 0.8084 (m-30) REVERT: A 1125 MET cc_start: 0.8127 (mtp) cc_final: 0.7827 (mtp) REVERT: A 1222 TYR cc_start: 0.7353 (t80) cc_final: 0.6809 (t80) REVERT: A 1240 TYR cc_start: 0.7553 (m-10) cc_final: 0.7185 (m-80) REVERT: A 1271 MET cc_start: 0.8718 (mmt) cc_final: 0.8483 (mmp) REVERT: A 1272 ASN cc_start: 0.7987 (m-40) cc_final: 0.7716 (m-40) REVERT: F 233 ILE cc_start: 0.8727 (mp) cc_final: 0.8463 (mp) REVERT: F 278 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7720 (mm-30) REVERT: F 801 TYR cc_start: 0.7904 (m-80) cc_final: 0.7588 (m-80) REVERT: F 878 ILE cc_start: 0.7797 (mm) cc_final: 0.7586 (mm) REVERT: C 227 MET cc_start: 0.3932 (mmm) cc_final: 0.1765 (tpt) REVERT: C 244 ASP cc_start: 0.7378 (t70) cc_final: 0.7064 (t0) REVERT: C 305 GLU cc_start: 0.8930 (pp20) cc_final: 0.8567 (pt0) REVERT: C 329 GLN cc_start: 0.6228 (mp10) cc_final: 0.5942 (mp10) REVERT: C 368 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8395 (tp40) REVERT: C 398 HIS cc_start: 0.6397 (t70) cc_final: 0.5989 (t70) outliers start: 39 outliers final: 22 residues processed: 323 average time/residue: 0.2812 time to fit residues: 146.7540 Evaluate side-chains 291 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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 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 F residue 994 LEU 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 14 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 194 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.145473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103090 restraints weight = 36788.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106288 restraints weight = 17750.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107067 restraints weight = 10592.219| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1959 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= 0.127 Angle : 0.586 12.873 26330 Z= 0.296 Chirality : 0.042 0.277 2981 Planarity : 0.004 0.066 3299 Dihedral : 7.093 58.933 2779 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.98 % Allowed : 15.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2292 helix: 0.79 (0.15), residues: 1210 sheet: -1.64 (0.35), residues: 220 loop : -1.55 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 185 HIS 0.007 0.001 HIS A1148 PHE 0.023 0.001 PHE A1004 TYR 0.015 0.001 TYR F 512 ARG 0.005 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 5) link_NAG-ASN : angle 1.20465 ( 15) hydrogen bonds : bond 0.03852 ( 915) hydrogen bonds : angle 4.62756 ( 2670) SS BOND : bond 0.00268 ( 7) SS BOND : angle 0.85266 ( 14) covalent geometry : bond 0.00283 (19463) covalent geometry : angle 0.58521 (26301) *********************** 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 329 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 1.959 Fit side-chains REVERT: A 433 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7711 (t0) REVERT: A 602 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7568 (mt-10) REVERT: A 762 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7736 (tp) REVERT: A 766 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.8004 (pt0) REVERT: A 936 PHE cc_start: 0.8060 (m-80) cc_final: 0.7603 (m-80) REVERT: A 1125 MET cc_start: 0.8118 (mtp) cc_final: 0.7834 (mtp) REVERT: A 1222 TYR cc_start: 0.7514 (t80) cc_final: 0.6832 (t80) REVERT: A 1240 TYR cc_start: 0.7473 (m-10) cc_final: 0.7061 (m-80) REVERT: A 1272 ASN cc_start: 0.8052 (m-40) cc_final: 0.7779 (m-40) REVERT: A 1526 ASN cc_start: 0.8046 (t0) cc_final: 0.7689 (t0) REVERT: F 233 ILE cc_start: 0.8748 (mp) cc_final: 0.8493 (mp) REVERT: F 278 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7826 (mm-30) REVERT: F 744 TYR cc_start: 0.6913 (t80) cc_final: 0.6529 (t80) REVERT: F 801 TYR cc_start: 0.7945 (m-80) cc_final: 0.7649 (m-80) REVERT: C 227 MET cc_start: 0.3777 (mmm) cc_final: 0.1580 (tpt) REVERT: C 244 ASP cc_start: 0.7366 (t70) cc_final: 0.7118 (t0) REVERT: C 329 GLN cc_start: 0.6245 (mp10) cc_final: 0.5963 (mp10) REVERT: C 351 GLN cc_start: 0.8951 (mp10) cc_final: 0.8723 (mp10) REVERT: C 368 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8493 (tp40) outliers start: 41 outliers final: 18 residues processed: 315 average time/residue: 0.2759 time to fit residues: 141.4024 Evaluate side-chains 290 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 433 ASP 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 655 LEU Chi-restraints excluded: chain A residue 707 ASP 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 966 LEU 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 330 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 864 HIS 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 129 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 668 ASN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.143664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101027 restraints weight = 36298.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105028 restraints weight = 18306.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105486 restraints weight = 10481.074| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19475 Z= 0.209 Angle : 0.648 12.773 26330 Z= 0.326 Chirality : 0.044 0.336 2981 Planarity : 0.004 0.063 3299 Dihedral : 7.273 58.211 2779 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.98 % Allowed : 16.81 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2292 helix: 0.69 (0.15), residues: 1210 sheet: -1.65 (0.35), residues: 220 loop : -1.61 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 821 HIS 0.004 0.001 HIS A1148 PHE 0.030 0.002 PHE A1507 TYR 0.017 0.002 TYR F 512 ARG 0.008 0.000 ARG A 623 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 5) link_NAG-ASN : angle 1.33144 ( 15) hydrogen bonds : bond 0.04014 ( 915) hydrogen bonds : angle 4.68711 ( 2670) SS BOND : bond 0.00316 ( 7) SS BOND : angle 1.08387 ( 14) covalent geometry : bond 0.00488 (19463) covalent geometry : angle 0.64716 (26301) *********************** 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 317 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 2.075 Fit side-chains revert: symmetry clash REVERT: A 433 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7794 (t0) REVERT: A 602 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7546 (mt-10) REVERT: A 762 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7811 (tp) REVERT: A 936 PHE cc_start: 0.8066 (m-80) cc_final: 0.7602 (m-80) REVERT: A 1029 ILE cc_start: 0.8867 (mt) cc_final: 0.8596 (mp) REVERT: A 1117 ASP cc_start: 0.7635 (p0) cc_final: 0.6961 (p0) REVERT: A 1125 MET cc_start: 0.8175 (mtp) cc_final: 0.7882 (mtp) REVERT: A 1222 TYR cc_start: 0.7534 (t80) cc_final: 0.6815 (t80) REVERT: A 1240 TYR cc_start: 0.7473 (m-10) cc_final: 0.7080 (m-80) REVERT: A 1271 MET cc_start: 0.8726 (mmt) cc_final: 0.8504 (mmp) REVERT: A 1272 ASN cc_start: 0.8080 (m-40) cc_final: 0.7836 (m-40) REVERT: A 1526 ASN cc_start: 0.8119 (t0) cc_final: 0.7743 (t0) REVERT: F 233 ILE cc_start: 0.8809 (mp) cc_final: 0.8533 (mp) REVERT: F 279 MET cc_start: 0.8742 (tpp) cc_final: 0.7841 (ttp) REVERT: F 646 GLU cc_start: 0.8397 (pm20) cc_final: 0.7986 (pm20) REVERT: F 744 TYR cc_start: 0.7058 (t80) cc_final: 0.6745 (t80) REVERT: F 801 TYR cc_start: 0.8057 (m-80) cc_final: 0.7835 (m-80) REVERT: C 227 MET cc_start: 0.3730 (mmm) cc_final: 0.1684 (tpt) REVERT: C 351 GLN cc_start: 0.8922 (mp10) cc_final: 0.8635 (mp10) REVERT: C 368 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8489 (tp40) outliers start: 41 outliers final: 33 residues processed: 304 average time/residue: 0.3822 time to fit residues: 191.9766 Evaluate side-chains 296 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 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 655 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 746 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1180 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 424 GLN Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 618 SER 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 F residue 1016 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 272 SER 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 33 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.145664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104280 restraints weight = 36213.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107159 restraints weight = 17224.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.108120 restraints weight = 10413.171| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19475 Z= 0.134 Angle : 0.605 13.628 26330 Z= 0.301 Chirality : 0.042 0.238 2981 Planarity : 0.004 0.061 3299 Dihedral : 7.112 59.691 2779 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.13 % Allowed : 17.58 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2292 helix: 0.78 (0.15), residues: 1212 sheet: -1.70 (0.36), residues: 210 loop : -1.52 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 821 HIS 0.004 0.001 HIS A1148 PHE 0.030 0.001 PHE A1507 TYR 0.014 0.001 TYR F 512 ARG 0.006 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 5) link_NAG-ASN : angle 1.19944 ( 15) hydrogen bonds : bond 0.03725 ( 915) hydrogen bonds : angle 4.56585 ( 2670) SS BOND : bond 0.00239 ( 7) SS BOND : angle 0.86079 ( 14) covalent geometry : bond 0.00305 (19463) covalent geometry : angle 0.60465 (26301) *********************** 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 326 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 282 time to evaluate : 2.416 Fit side-chains revert: symmetry clash REVERT: A 433 ASP cc_start: 0.8053 (m-30) cc_final: 0.7640 (t0) REVERT: A 602 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7495 (mt-10) REVERT: A 707 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7482 (t0) REVERT: A 742 TYR cc_start: 0.8467 (t80) cc_final: 0.8264 (t80) REVERT: A 936 PHE cc_start: 0.8123 (m-80) cc_final: 0.7642 (m-80) REVERT: A 1117 ASP cc_start: 0.7552 (p0) cc_final: 0.6996 (p0) REVERT: A 1222 TYR cc_start: 0.7549 (t80) cc_final: 0.6846 (t80) REVERT: A 1240 TYR cc_start: 0.7381 (m-10) cc_final: 0.6992 (m-80) REVERT: A 1258 MET cc_start: 0.7711 (ttm) cc_final: 0.7394 (ttm) REVERT: A 1272 ASN cc_start: 0.8069 (m-40) cc_final: 0.7795 (m-40) REVERT: A 1446 ASN cc_start: 0.8395 (p0) cc_final: 0.8053 (p0) REVERT: A 1526 ASN cc_start: 0.8111 (t0) cc_final: 0.7716 (t0) REVERT: F 233 ILE cc_start: 0.8790 (mp) cc_final: 0.8509 (mp) REVERT: F 278 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7693 (mm-30) REVERT: F 594 SER cc_start: 0.8926 (t) cc_final: 0.8523 (p) REVERT: F 744 TYR cc_start: 0.6983 (t80) cc_final: 0.6690 (t80) REVERT: C 227 MET cc_start: 0.3786 (mmm) cc_final: 0.1766 (tpt) REVERT: C 351 GLN cc_start: 0.8784 (mp10) cc_final: 0.8504 (mp10) outliers start: 44 outliers final: 28 residues processed: 309 average time/residue: 0.3152 time to fit residues: 157.9079 Evaluate side-chains 291 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 2.245 ------------------------------------------------------------------------------- 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 265 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 525 VAL 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 655 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 746 ASN 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 469 ILE Chi-restraints excluded: chain F residue 618 SER 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 82 optimal weight: 0.8980 chunk 196 optimal weight: 0.0030 chunk 12 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 146 optimal weight: 0.8980 chunk 185 optimal weight: 0.0980 chunk 17 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.146443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.103007 restraints weight = 36438.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106317 restraints weight = 16585.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.108420 restraints weight = 10519.034| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2436 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 : 0.593 14.166 26330 Z= 0.296 Chirality : 0.042 0.242 2981 Planarity : 0.004 0.060 3299 Dihedral : 6.893 59.294 2779 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.13 % Allowed : 18.45 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2292 helix: 0.87 (0.15), residues: 1217 sheet: -1.49 (0.35), residues: 220 loop : -1.49 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 821 HIS 0.008 0.001 HIS A1148 PHE 0.035 0.001 PHE A1507 TYR 0.014 0.001 TYR F 719 ARG 0.007 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 5) link_NAG-ASN : angle 1.13998 ( 15) hydrogen bonds : bond 0.03543 ( 915) hydrogen bonds : angle 4.46061 ( 2670) SS BOND : bond 0.00209 ( 7) SS BOND : angle 0.75847 ( 14) covalent geometry : bond 0.00255 (19463) covalent geometry : angle 0.59245 (26301) *********************** 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 343 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 1.965 Fit side-chains REVERT: A 199 ASP cc_start: 0.9010 (t0) cc_final: 0.8774 (t0) REVERT: A 602 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7496 (mt-10) REVERT: A 909 PHE cc_start: 0.7970 (m-80) cc_final: 0.7752 (m-80) REVERT: A 931 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7141 (t70) REVERT: A 936 PHE cc_start: 0.8051 (m-80) cc_final: 0.7629 (m-80) REVERT: A 1029 ILE cc_start: 0.8766 (mt) cc_final: 0.8525 (mp) REVERT: A 1222 TYR cc_start: 0.7524 (t80) cc_final: 0.6862 (t80) REVERT: A 1240 TYR cc_start: 0.7289 (m-10) cc_final: 0.6885 (m-80) REVERT: A 1258 MET cc_start: 0.7872 (ttm) cc_final: 0.7425 (ttm) REVERT: A 1272 ASN cc_start: 0.7992 (m-40) cc_final: 0.7707 (m-40) REVERT: A 1446 ASN cc_start: 0.8330 (p0) cc_final: 0.7999 (p0) REVERT: A 1526 ASN cc_start: 0.8070 (t0) cc_final: 0.7730 (t0) REVERT: A 1615 ARG cc_start: 0.4418 (ptt180) cc_final: 0.4210 (ptt180) REVERT: F 233 ILE cc_start: 0.8770 (mp) cc_final: 0.8479 (mp) REVERT: F 594 SER cc_start: 0.8883 (t) cc_final: 0.8498 (p) REVERT: C 227 MET cc_start: 0.3683 (mmm) cc_final: 0.1806 (tpt) REVERT: C 351 GLN cc_start: 0.8814 (mp10) cc_final: 0.8548 (mp10) REVERT: C 369 MET cc_start: 0.9183 (ppp) cc_final: 0.8951 (ppp) outliers start: 44 outliers final: 30 residues processed: 323 average time/residue: 0.2917 time to fit residues: 152.3241 Evaluate side-chains 304 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 265 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 395 PHE 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 572 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 1255 CYS Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 707 LEU Chi-restraints excluded: chain F residue 793 MET 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 C residue 299 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 96 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 227 optimal weight: 20.0000 chunk 147 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 116 optimal weight: 0.0030 chunk 186 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1356 HIS ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.146174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104109 restraints weight = 35759.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.107370 restraints weight = 16067.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109389 restraints weight = 10100.285| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2565 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= 0.123 Angle : 0.604 14.361 26330 Z= 0.301 Chirality : 0.042 0.242 2981 Planarity : 0.004 0.058 3299 Dihedral : 6.804 58.401 2779 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.17 % Allowed : 18.94 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2292 helix: 0.95 (0.15), residues: 1211 sheet: -1.43 (0.36), residues: 220 loop : -1.43 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 821 HIS 0.007 0.001 HIS A1148 PHE 0.030 0.001 PHE A1507 TYR 0.015 0.001 TYR F 744 ARG 0.011 0.000 ARG F 643 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 5) link_NAG-ASN : angle 1.13488 ( 15) hydrogen bonds : bond 0.03482 ( 915) hydrogen bonds : angle 4.44747 ( 2670) SS BOND : bond 0.00223 ( 7) SS BOND : angle 0.76785 ( 14) covalent geometry : bond 0.00278 (19463) covalent geometry : angle 0.60371 (26301) *********************** 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 330 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 2.092 Fit side-chains REVERT: A 173 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7336 (tm-30) REVERT: A 199 ASP cc_start: 0.8982 (t0) cc_final: 0.8743 (t0) REVERT: A 291 MET cc_start: 0.7595 (tpt) cc_final: 0.7112 (tpp) REVERT: A 433 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7714 (t0) REVERT: A 707 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7461 (t0) REVERT: A 909 PHE cc_start: 0.7966 (m-80) cc_final: 0.7711 (m-80) REVERT: A 931 HIS cc_start: 0.8072 (OUTLIER) cc_final: 0.7415 (t70) REVERT: A 936 PHE cc_start: 0.8085 (m-80) cc_final: 0.7672 (m-80) REVERT: A 1029 ILE cc_start: 0.8752 (mt) cc_final: 0.8503 (mp) REVERT: A 1222 TYR cc_start: 0.7452 (t80) cc_final: 0.6849 (t80) REVERT: A 1240 TYR cc_start: 0.7332 (m-10) cc_final: 0.6927 (m-80) REVERT: A 1258 MET cc_start: 0.7922 (ttm) cc_final: 0.7447 (ttm) REVERT: A 1272 ASN cc_start: 0.7971 (m-40) cc_final: 0.7706 (m-40) REVERT: A 1526 ASN cc_start: 0.8132 (t0) cc_final: 0.7734 (t0) REVERT: A 1611 PHE cc_start: 0.7914 (t80) cc_final: 0.7702 (t80) REVERT: F 233 ILE cc_start: 0.8776 (mp) cc_final: 0.8487 (mp) REVERT: F 278 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7603 (mm-30) REVERT: F 594 SER cc_start: 0.8902 (t) cc_final: 0.8509 (p) REVERT: F 744 TYR cc_start: 0.6988 (t80) cc_final: 0.6697 (t80) REVERT: F 827 LYS cc_start: 0.8878 (tppt) cc_final: 0.8638 (ttpt) REVERT: F 861 MET cc_start: 0.7102 (mtt) cc_final: 0.6552 (mtt) REVERT: C 227 MET cc_start: 0.3621 (mmm) cc_final: 0.1704 (tpt) REVERT: C 351 GLN cc_start: 0.8809 (mp10) cc_final: 0.8532 (mp10) REVERT: C 369 MET cc_start: 0.9188 (ppp) cc_final: 0.8892 (ppp) outliers start: 45 outliers final: 33 residues processed: 310 average time/residue: 0.3284 time to fit residues: 164.7249 Evaluate side-chains 312 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 2.054 ------------------------------------------------------------------------------- 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 172 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 395 PHE 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 655 LEU Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain A residue 746 ASN 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 1255 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 469 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 883 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 187 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.144236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101455 restraints weight = 36976.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104468 restraints weight = 18252.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105479 restraints weight = 10835.479| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19475 Z= 0.182 Angle : 0.639 13.820 26330 Z= 0.319 Chirality : 0.044 0.261 2981 Planarity : 0.004 0.057 3299 Dihedral : 6.935 58.199 2779 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.03 % Allowed : 19.28 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2292 helix: 0.89 (0.15), residues: 1213 sheet: -1.57 (0.37), residues: 210 loop : -1.46 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 821 HIS 0.007 0.001 HIS A1148 PHE 0.034 0.002 PHE A1507 TYR 0.016 0.001 TYR F 719 ARG 0.007 0.000 ARG C 257 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 5) link_NAG-ASN : angle 1.23448 ( 15) hydrogen bonds : bond 0.03682 ( 915) hydrogen bonds : angle 4.53995 ( 2670) SS BOND : bond 0.00284 ( 7) SS BOND : angle 1.01726 ( 14) covalent geometry : bond 0.00425 (19463) covalent geometry : angle 0.63874 (26301) *********************** 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 315 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 3.741 Fit side-chains REVERT: A 433 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7763 (t0) REVERT: A 707 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7539 (t0) REVERT: A 931 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7374 (t70) REVERT: A 936 PHE cc_start: 0.8190 (m-80) cc_final: 0.7759 (m-80) REVERT: A 1029 ILE cc_start: 0.8741 (mt) cc_final: 0.8493 (mp) REVERT: A 1222 TYR cc_start: 0.7651 (t80) cc_final: 0.6930 (t80) REVERT: A 1240 TYR cc_start: 0.7281 (m-10) cc_final: 0.6831 (m-80) REVERT: A 1258 MET cc_start: 0.7924 (ttm) cc_final: 0.7484 (ttm) REVERT: A 1272 ASN cc_start: 0.8059 (m-40) cc_final: 0.7753 (m-40) REVERT: A 1446 ASN cc_start: 0.8525 (p0) cc_final: 0.8154 (p0) REVERT: A 1526 ASN cc_start: 0.8213 (t0) cc_final: 0.7804 (t0) REVERT: F 233 ILE cc_start: 0.8782 (mp) cc_final: 0.8475 (mp) REVERT: F 499 ARG cc_start: 0.7499 (ptp90) cc_final: 0.7283 (ptp-170) REVERT: F 594 SER cc_start: 0.8960 (t) cc_final: 0.8528 (p) REVERT: F 744 TYR cc_start: 0.7050 (t80) cc_final: 0.6738 (t80) REVERT: C 227 MET cc_start: 0.3677 (mmm) cc_final: 0.1700 (tpt) REVERT: C 301 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7774 (mm110) outliers start: 42 outliers final: 35 residues processed: 298 average time/residue: 0.3959 time to fit residues: 194.0974 Evaluate side-chains 298 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 2.434 ------------------------------------------------------------------------------- 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 172 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 365 TRP Chi-restraints excluded: chain A residue 395 PHE 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 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 1004 PHE Chi-restraints excluded: chain A residue 1068 VAL 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 A residue 1439 THR Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 469 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 883 MET Chi-restraints excluded: chain F residue 994 LEU 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 301 GLN 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 173 optimal weight: 3.9990 chunk 157 optimal weight: 0.0970 chunk 224 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 66 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.146371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103893 restraints weight = 36507.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107274 restraints weight = 17271.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107809 restraints weight = 10185.436| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19475 Z= 0.127 Angle : 0.620 14.641 26330 Z= 0.309 Chirality : 0.043 0.236 2981 Planarity : 0.004 0.058 3299 Dihedral : 6.789 57.487 2779 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.88 % Allowed : 19.95 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2292 helix: 0.96 (0.15), residues: 1210 sheet: -1.30 (0.36), residues: 215 loop : -1.45 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 821 HIS 0.006 0.001 HIS A1148 PHE 0.036 0.001 PHE A1611 TYR 0.017 0.001 TYR A 583 ARG 0.008 0.000 ARG F 643 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 5) link_NAG-ASN : angle 1.12942 ( 15) hydrogen bonds : bond 0.03509 ( 915) hydrogen bonds : angle 4.48884 ( 2670) SS BOND : bond 0.00203 ( 7) SS BOND : angle 0.80739 ( 14) covalent geometry : bond 0.00290 (19463) covalent geometry : angle 0.61984 (26301) ********************** 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 310 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 2.387 Fit side-chains REVERT: A 433 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7756 (t0) REVERT: A 588 PHE cc_start: 0.7925 (t80) cc_final: 0.7557 (t80) REVERT: A 634 TRP cc_start: 0.6163 (m-90) cc_final: 0.5789 (m-90) REVERT: A 931 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7309 (t70) REVERT: A 936 PHE cc_start: 0.8190 (m-80) cc_final: 0.7749 (m-80) REVERT: A 1029 ILE cc_start: 0.8718 (mt) cc_final: 0.8470 (mp) REVERT: A 1222 TYR cc_start: 0.7682 (t80) cc_final: 0.6984 (t80) REVERT: A 1240 TYR cc_start: 0.7251 (m-10) cc_final: 0.6776 (m-80) REVERT: A 1258 MET cc_start: 0.7993 (ttm) cc_final: 0.7623 (ttm) REVERT: A 1272 ASN cc_start: 0.8028 (m-40) cc_final: 0.7812 (m-40) REVERT: A 1526 ASN cc_start: 0.8196 (t0) cc_final: 0.7726 (t0) REVERT: F 233 ILE cc_start: 0.8818 (mp) cc_final: 0.8532 (mp) REVERT: F 278 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7682 (mm-30) REVERT: F 297 ASN cc_start: 0.7648 (m-40) cc_final: 0.7436 (m-40) REVERT: F 499 ARG cc_start: 0.7461 (ptp90) cc_final: 0.7240 (ptp-170) REVERT: F 594 SER cc_start: 0.8929 (t) cc_final: 0.8534 (p) REVERT: F 744 TYR cc_start: 0.6974 (t80) cc_final: 0.6678 (t80) REVERT: F 861 MET cc_start: 0.6988 (mtt) cc_final: 0.6447 (mtt) REVERT: C 227 MET cc_start: 0.3741 (mmm) cc_final: 0.1739 (tpt) outliers start: 39 outliers final: 32 residues processed: 293 average time/residue: 0.2832 time to fit residues: 134.0704 Evaluate side-chains 299 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 2.102 ------------------------------------------------------------------------------- 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 205 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 395 PHE 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 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 1068 VAL Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1470 MET Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 469 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 883 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 63 optimal weight: 4.9990 chunk 189 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.146580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104121 restraints weight = 36429.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107492 restraints weight = 17165.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107986 restraints weight = 10218.794| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19475 Z= 0.127 Angle : 0.622 14.682 26330 Z= 0.308 Chirality : 0.043 0.326 2981 Planarity : 0.004 0.057 3299 Dihedral : 6.740 57.413 2779 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.69 % Allowed : 20.24 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2292 helix: 1.01 (0.15), residues: 1205 sheet: -1.28 (0.36), residues: 215 loop : -1.42 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 821 HIS 0.006 0.001 HIS A1148 PHE 0.029 0.001 PHE F 780 TYR 0.016 0.001 TYR F 719 ARG 0.011 0.000 ARG F 643 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 5) link_NAG-ASN : angle 1.10952 ( 15) hydrogen bonds : bond 0.03462 ( 915) hydrogen bonds : angle 4.48189 ( 2670) SS BOND : bond 0.00214 ( 7) SS BOND : angle 0.80675 ( 14) covalent geometry : bond 0.00291 (19463) covalent geometry : angle 0.62178 (26301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7839.48 seconds wall clock time: 140 minutes 46.40 seconds (8446.40 seconds total)