Starting phenix.real_space_refine on Tue May 20 20:52:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c8g_16475/05_2025/8c8g_16475.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c8g_16475/05_2025/8c8g_16475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c8g_16475/05_2025/8c8g_16475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c8g_16475/05_2025/8c8g_16475.map" model { file = "/net/cci-nas-00/data/ceres_data/8c8g_16475/05_2025/8c8g_16475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c8g_16475/05_2025/8c8g_16475.cif" } resolution = 2.98 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 12995 2.51 5 N 3303 2.21 5 O 4013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20362 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10790 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 37, 'TRANS': 1297} Chain: "B" Number of atoms: 9572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9572 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 39, 'TRANS': 1155} Time building chain proxies: 11.46, per 1000 atoms: 0.56 Number of scatterers: 20362 At special positions: 0 Unit cell: (127.92, 116.44, 151.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 4013 8.00 N 3303 7.00 C 12995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 366 " distance=2.07 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 Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 2.6 seconds 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 36 sheets defined 26.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 100 through 122 Processing helix chain 'A' and resid 126 through 138 removed outlier: 3.813A pdb=" N PHE A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.907A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.590A pdb=" N SER A 335 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 356 through 367 Processing helix chain 'A' and resid 373 through 376 removed outlier: 3.975A pdb=" N LYS A 376 " --> pdb=" O GLN A 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 373 through 376' Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.531A pdb=" N THR A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 414 " --> pdb=" O TYR A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.656A pdb=" N PHE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.574A pdb=" N GLU A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 639 Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 716 through 750 removed outlier: 4.019A pdb=" N VAL A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 781 removed outlier: 3.525A pdb=" N THR A 774 " --> pdb=" O LYS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 801 Processing helix chain 'A' and resid 803 through 830 Processing helix chain 'A' and resid 830 through 861 removed outlier: 3.565A pdb=" N GLN A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 883 through 905 removed outlier: 3.510A pdb=" N VAL A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 897 " --> pdb=" O HIS A 893 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 902 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1133 removed outlier: 3.865A pdb=" N HIS A1133 " --> pdb=" O PHE A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1290 Processing helix chain 'B' and resid 69 through 88 removed outlier: 3.537A pdb=" N LEU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 101 Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.530A pdb=" N SER B 155 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.531A pdb=" N GLY B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.569A pdb=" N ALA B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.647A pdb=" N TYR B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 391 through 397 removed outlier: 3.642A pdb=" N THR B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.558A pdb=" N ALA B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.815A pdb=" N ILE B 450 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 removed outlier: 4.522A pdb=" N ASP B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.075A pdb=" N PHE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 528 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 562 through 575 removed outlier: 4.264A pdb=" N TYR B 566 " --> pdb=" O GLN B 562 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 568 " --> pdb=" O LYS B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 603 removed outlier: 3.809A pdb=" N LEU B 582 " --> pdb=" O ARG B 578 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 603 " --> pdb=" O SER B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 650 removed outlier: 3.531A pdb=" N TYR B 626 " --> pdb=" O TYR B 622 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 648 " --> pdb=" O VAL B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 665 through 674 removed outlier: 3.653A pdb=" N LEU B 671 " --> pdb=" O ASP B 667 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 41 removed outlier: 6.896A pdb=" N ILE A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 186 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 167 removed outlier: 3.926A pdb=" N GLY A 179 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 166 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS A 177 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.511A pdb=" N THR A 451 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 282 Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 371 removed outlier: 3.520A pdb=" N LYS A 370 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 477 removed outlier: 7.734A pdb=" N VAL A 560 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLU A 464 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 562 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU A 466 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 589 Processing sheet with id=AB1, first strand: chain 'A' and resid 644 through 645 Processing sheet with id=AB2, first strand: chain 'A' and resid 923 through 924 Processing sheet with id=AB3, first strand: chain 'A' and resid 941 through 944 removed outlier: 3.967A pdb=" N VAL A 976 " --> pdb=" O PHE A1099 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE A1011 " --> pdb=" O TYR A1102 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A1029 " --> pdb=" O ILE A1011 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A1013 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A1027 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER A1015 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU A1025 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A1017 " --> pdb=" O GLU A1023 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU A1023 " --> pdb=" O VAL A1017 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A1036 " --> pdb=" O ILE A1051 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 952 through 953 removed outlier: 10.918A pdb=" N GLN A 958 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP A1112 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU A1110 " --> pdb=" O ARG A 999 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG A 999 " --> pdb=" O LEU A1110 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ASP A1112 " --> pdb=" O TRP A 997 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP A 997 " --> pdb=" O ASP A1112 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A1072 " --> pdb=" O LEU A1083 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU A1083 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A1074 " --> pdb=" O LEU A1081 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1220 through 1223 Processing sheet with id=AB6, first strand: chain 'A' and resid 1160 through 1161 Processing sheet with id=AB7, first strand: chain 'A' and resid 1179 through 1180 Processing sheet with id=AB8, first strand: chain 'A' and resid 1229 through 1235 Processing sheet with id=AB9, first strand: chain 'A' and resid 1259 through 1261 removed outlier: 5.194A pdb=" N LEU A1273 " --> pdb=" O ILE A1297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1278 through 1279 Processing sheet with id=AC2, first strand: chain 'B' and resid 125 through 130 removed outlier: 3.991A pdb=" N HIS B 127 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B 117 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN B 9 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU B 23 " --> pdb=" O TYR B 12 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TRP B 35 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL B 134 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.569A pdb=" N ARG B 179 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE B 172 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 207 through 212 removed outlier: 6.539A pdb=" N TYR B 219 " --> pdb=" O PHE B 210 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 340 through 341 removed outlier: 6.263A pdb=" N LYS B 340 " --> pdb=" O THR B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 502 through 503 Processing sheet with id=AC8, first strand: chain 'B' and resid 690 through 694 removed outlier: 7.638A pdb=" N SER B 711 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU B 702 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N GLU B 708 " --> pdb=" O ASN B 739 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN B 739 " --> pdb=" O GLU B 708 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 736 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 718 removed outlier: 6.592A pdb=" N LEU B 850 " --> pdb=" O LYS B 756 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS B 756 " --> pdb=" O LEU B 850 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 852 " --> pdb=" O THR B 754 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ASP B 815 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU B 821 " --> pdb=" O ASP B 815 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 943 through 947 removed outlier: 7.989A pdb=" N LEU B 928 " --> pdb=" O GLU B 888 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU B 888 " --> pdb=" O LEU B 928 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 902 through 905 removed outlier: 4.381A pdb=" N LEU B1011 " --> pdb=" O PRO B 912 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 955 through 959 removed outlier: 3.523A pdb=" N TYR B 955 " --> pdb=" O VAL B 966 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 988 through 992 Processing sheet with id=AD5, first strand: chain 'B' and resid 1047 through 1050 Processing sheet with id=AD6, first strand: chain 'B' and resid 1055 through 1056 removed outlier: 6.515A pdb=" N LEU B1055 " --> pdb=" O LYS B1121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1085 through 1088 Processing sheet with id=AD8, first strand: chain 'B' and resid 1126 through 1128 removed outlier: 3.979A pdb=" N SER B1126 " --> pdb=" O ILE B1150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1132 through 1133 removed outlier: 6.995A pdb=" N SER B1132 " --> pdb=" O THR B1198 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR B1184 " --> pdb=" O ILE B1191 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B1193 " --> pdb=" O PHE B1182 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B1181 " --> pdb=" O GLU B1167 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1947 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: 8.79 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3527 1.31 - 1.44: 5482 1.44 - 1.57: 11675 1.57 - 1.71: 0 1.71 - 1.84: 93 Bond restraints: 20777 Sorted by residual: bond pdb=" C PRO B 209 " pdb=" O PRO B 209 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.16e-02 7.43e+03 2.76e+01 bond pdb=" C PRO A1329 " pdb=" O PRO A1329 " ideal model delta sigma weight residual 1.233 1.179 0.054 1.12e-02 7.97e+03 2.32e+01 bond pdb=" CA SER B 233 " pdb=" CB SER B 233 " ideal model delta sigma weight residual 1.527 1.460 0.067 1.44e-02 4.82e+03 2.16e+01 bond pdb=" CA SER B1020 " pdb=" CB SER B1020 " ideal model delta sigma weight residual 1.530 1.463 0.067 1.55e-02 4.16e+03 1.86e+01 bond pdb=" CA SER A1230 " pdb=" CB SER A1230 " ideal model delta sigma weight residual 1.536 1.451 0.085 2.08e-02 2.31e+03 1.66e+01 ... (remaining 20772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 23489 2.06 - 4.12: 4384 4.12 - 6.18: 245 6.18 - 8.24: 18 8.24 - 10.30: 3 Bond angle restraints: 28139 Sorted by residual: angle pdb=" N PRO B 241 " pdb=" CA PRO B 241 " pdb=" CB PRO B 241 " ideal model delta sigma weight residual 103.25 92.95 10.30 1.05e+00 9.07e-01 9.62e+01 angle pdb=" N ARG A1301 " pdb=" CA ARG A1301 " pdb=" C ARG A1301 " ideal model delta sigma weight residual 110.53 102.99 7.54 1.29e+00 6.01e-01 3.42e+01 angle pdb=" N ARG A1301 " pdb=" CA ARG A1301 " pdb=" CB ARG A1301 " ideal model delta sigma weight residual 110.44 118.78 -8.34 1.43e+00 4.89e-01 3.40e+01 angle pdb=" N GLN B 281 " pdb=" CA GLN B 281 " pdb=" C GLN B 281 " ideal model delta sigma weight residual 114.31 107.26 7.05 1.29e+00 6.01e-01 2.99e+01 angle pdb=" N VAL A 84 " pdb=" CA VAL A 84 " pdb=" C VAL A 84 " ideal model delta sigma weight residual 113.71 108.63 5.08 9.50e-01 1.11e+00 2.86e+01 ... (remaining 28134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 11218 17.88 - 35.76: 1077 35.76 - 53.63: 160 53.63 - 71.51: 31 71.51 - 89.39: 11 Dihedral angle restraints: 12497 sinusoidal: 5033 harmonic: 7464 Sorted by residual: dihedral pdb=" CA ASN B 846 " pdb=" C ASN B 846 " pdb=" N GLU B 847 " pdb=" CA GLU B 847 " ideal model delta harmonic sigma weight residual -180.00 -150.18 -29.82 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA LYS A 964 " pdb=" C LYS A 964 " pdb=" N ASP A 965 " pdb=" CA ASP A 965 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA PRO B 686 " pdb=" C PRO B 686 " pdb=" N SER B 687 " pdb=" CA SER B 687 " ideal model delta harmonic sigma weight residual 180.00 -152.12 -27.88 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 12494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1574 0.060 - 0.120: 1095 0.120 - 0.181: 409 0.181 - 0.241: 54 0.241 - 0.301: 9 Chirality restraints: 3141 Sorted by residual: chirality pdb=" CA VAL B 823 " pdb=" N VAL B 823 " pdb=" C VAL B 823 " pdb=" CB VAL B 823 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA ILE B 896 " pdb=" N ILE B 896 " pdb=" C ILE B 896 " pdb=" CB ILE B 896 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PHE B 244 " pdb=" N PHE B 244 " pdb=" C PHE B 244 " pdb=" CB PHE B 244 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3138 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1099 " -0.043 2.00e-02 2.50e+03 2.97e-02 1.54e+01 pdb=" CG PHE A1099 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A1099 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A1099 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A1099 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A1099 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 989 " -0.047 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR B 989 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 989 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 989 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 989 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 989 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 989 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 989 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1039 " -0.045 2.00e-02 2.50e+03 2.38e-02 1.14e+01 pdb=" CG TYR B1039 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR B1039 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B1039 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B1039 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B1039 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B1039 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1039 " -0.022 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1767 2.74 - 3.28: 19591 3.28 - 3.82: 32663 3.82 - 4.36: 46348 4.36 - 4.90: 74298 Nonbonded interactions: 174667 Sorted by model distance: nonbonded pdb=" O LEU B 239 " pdb=" C GLN B 240 " model vdw 2.198 3.270 nonbonded pdb=" O LEU B 93 " pdb=" OG1 THR B 97 " model vdw 2.209 3.040 nonbonded pdb=" O LYS A 813 " pdb=" OG1 THR A 817 " model vdw 2.251 3.040 nonbonded pdb=" O ALA B 111 " pdb=" OG1 THR B 115 " model vdw 2.268 3.040 nonbonded pdb=" OD2 ASP A 243 " pdb=" OG1 THR A 245 " model vdw 2.277 3.040 ... (remaining 174662 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 46.180 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 0.013 0.085 20778 Z= 0.897 Angle : 1.498 10.297 28141 Z= 1.049 Chirality : 0.083 0.301 3141 Planarity : 0.007 0.057 3624 Dihedral : 14.188 89.389 7688 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.96 % Favored : 91.81 % Rotamer: Outliers : 0.88 % Allowed : 5.92 % Favored : 93.20 % Cbeta Deviations : 0.04 % 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: -4.21 (0.13), residues: 2526 helix: -3.95 (0.11), residues: 638 sheet: -2.36 (0.23), residues: 444 loop : -2.40 (0.14), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.009 TRP B 631 HIS 0.035 0.004 HIS A 922 PHE 0.053 0.007 PHE A1099 TYR 0.050 0.008 TYR A1108 ARG 0.018 0.002 ARG A 766 Details of bonding type rmsd hydrogen bonds : bond 0.26048 ( 694) hydrogen bonds : angle 10.97668 ( 1947) SS BOND : bond 0.03999 ( 1) SS BOND : angle 4.95621 ( 2) covalent geometry : bond 0.01284 (20777) covalent geometry : angle 1.49727 (28139) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 365 time to evaluate : 2.441 Fit side-chains revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8616 (m110) cc_final: 0.8409 (m-40) REVERT: A 46 GLU cc_start: 0.8087 (tt0) cc_final: 0.7793 (tt0) REVERT: A 48 ARG cc_start: 0.6935 (ptp-110) cc_final: 0.6414 (ptp-110) REVERT: A 94 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7758 (mtm-85) REVERT: A 228 SER cc_start: 0.8822 (m) cc_final: 0.8556 (t) REVERT: A 251 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: A 383 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7176 (ttt-90) REVERT: A 387 ARG cc_start: 0.8569 (ttm170) cc_final: 0.8130 (mtp85) REVERT: A 505 ASP cc_start: 0.7714 (t0) cc_final: 0.7457 (t0) REVERT: A 530 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7172 (mtm110) REVERT: A 554 ASP cc_start: 0.8579 (t70) cc_final: 0.8267 (t0) REVERT: A 576 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6769 (tm) REVERT: A 611 MET cc_start: 0.8574 (mtm) cc_final: 0.8175 (mtt) REVERT: A 615 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7126 (mp0) REVERT: A 645 GLU cc_start: 0.9008 (mp0) cc_final: 0.8745 (mp0) REVERT: A 711 TYR cc_start: 0.6992 (t80) cc_final: 0.6674 (t80) REVERT: A 834 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7868 (tttp) REVERT: A 868 TYR cc_start: 0.8443 (t80) cc_final: 0.7833 (t80) REVERT: A 876 ARG cc_start: 0.8770 (ttp-110) cc_final: 0.8570 (mtm110) REVERT: A 971 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8087 (ttpp) REVERT: A 1209 MET cc_start: 0.6007 (ptt) cc_final: 0.4620 (tmm) REVERT: B 11 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7862 (ttp-170) REVERT: B 107 LYS cc_start: 0.8147 (tppp) cc_final: 0.7692 (ttpt) REVERT: B 151 SER cc_start: 0.8470 (m) cc_final: 0.8233 (t) REVERT: B 207 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7999 (mtm-85) REVERT: B 239 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8306 (tt) REVERT: B 253 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7868 (tttm) REVERT: B 274 GLN cc_start: 0.8950 (mt0) cc_final: 0.8584 (mt0) REVERT: B 425 GLU cc_start: 0.7620 (mp0) cc_final: 0.7271 (mp0) REVERT: B 479 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7509 (pp20) REVERT: B 508 THR cc_start: 0.7368 (t) cc_final: 0.7144 (p) REVERT: B 712 ASN cc_start: 0.8440 (t0) cc_final: 0.8048 (t0) REVERT: B 714 SER cc_start: 0.8546 (t) cc_final: 0.8198 (t) REVERT: B 780 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8509 (mt-10) REVERT: B 900 MET cc_start: 0.7627 (ptp) cc_final: 0.7247 (ptt) REVERT: B 952 GLU cc_start: 0.8171 (mp0) cc_final: 0.7348 (tp30) REVERT: B 1026 MET cc_start: 0.6121 (mtp) cc_final: 0.5919 (mtm) REVERT: B 1053 SER cc_start: 0.8156 (t) cc_final: 0.7424 (p) REVERT: B 1062 LEU cc_start: 0.8355 (mt) cc_final: 0.8118 (mt) REVERT: B 1077 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8445 (tm-30) outliers start: 20 outliers final: 5 residues processed: 377 average time/residue: 1.1298 time to fit residues: 491.0398 Evaluate side-chains 258 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 250 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 PRO Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 782 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 197 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 137 GLN A 140 ASN A 184 ASN A 257 HIS A 303 HIS A 381 ASN A 445 GLN A 534 ASN A 572 HIS A 619 GLN A 632 GLN A 730 GLN A 745 GLN A 819 ASN A 860 ASN A 931 GLN A 955 HIS A1067 ASN A1264 ASN B 145 ASN B 212 GLN B 524 GLN B 570 GLN B 591 ASN B 643 GLN B 733 ASN B 777 ASN B 825 HIS B 863 ASN B 873 ASN B 908 ASN B1059 ASN B1135 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119950 restraints weight = 23652.751| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.82 r_work: 0.3289 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20778 Z= 0.129 Angle : 0.564 10.580 28141 Z= 0.309 Chirality : 0.044 0.161 3141 Planarity : 0.004 0.100 3624 Dihedral : 6.244 57.291 2751 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 2.59 % Allowed : 11.27 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.15), residues: 2526 helix: -1.51 (0.18), residues: 641 sheet: -1.87 (0.22), residues: 481 loop : -1.86 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 629 HIS 0.006 0.001 HIS A 922 PHE 0.024 0.001 PHE B 438 TYR 0.018 0.001 TYR A1108 ARG 0.004 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 694) hydrogen bonds : angle 5.78318 ( 1947) SS BOND : bond 0.00168 ( 1) SS BOND : angle 2.22112 ( 2) covalent geometry : bond 0.00291 (20777) covalent geometry : angle 0.56343 (28139) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 2.351 Fit side-chains REVERT: A 10 ASN cc_start: 0.8311 (m110) cc_final: 0.8020 (m-40) REVERT: A 48 ARG cc_start: 0.6771 (ptp-110) cc_final: 0.6064 (ptp-110) REVERT: A 94 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7674 (mtm-85) REVERT: A 447 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8344 (pt) REVERT: A 471 GLN cc_start: 0.7734 (pp30) cc_final: 0.7458 (pp30) REVERT: A 530 ARG cc_start: 0.7374 (mtt90) cc_final: 0.6995 (mtm110) REVERT: A 576 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6711 (tm) REVERT: A 593 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7935 (mm-30) REVERT: A 615 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7255 (pt0) REVERT: A 639 ASN cc_start: 0.8522 (m-40) cc_final: 0.8248 (m-40) REVERT: A 653 ASP cc_start: 0.6741 (m-30) cc_final: 0.5873 (t0) REVERT: A 711 TYR cc_start: 0.7149 (t80) cc_final: 0.6883 (t80) REVERT: A 808 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7906 (mtp) REVERT: A 834 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7872 (tttt) REVERT: A 868 TYR cc_start: 0.8194 (t80) cc_final: 0.7614 (t80) REVERT: A 876 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8391 (mtm110) REVERT: A 971 LYS cc_start: 0.8417 (ttmt) cc_final: 0.7981 (tttm) REVERT: A 980 ASN cc_start: 0.7929 (m110) cc_final: 0.7647 (m110) REVERT: A 1209 MET cc_start: 0.5508 (ptt) cc_final: 0.4058 (tmm) REVERT: A 1288 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7401 (tttp) REVERT: B 94 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7602 (mp0) REVERT: B 207 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7841 (mtm-85) REVERT: B 253 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7674 (tttm) REVERT: B 274 GLN cc_start: 0.8447 (mt0) cc_final: 0.8142 (mt0) REVERT: B 326 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: B 425 GLU cc_start: 0.7391 (mp0) cc_final: 0.6981 (mp0) REVERT: B 479 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7147 (pp20) REVERT: B 627 MET cc_start: 0.9090 (mtm) cc_final: 0.8724 (mtp) REVERT: B 648 ILE cc_start: 0.8286 (pt) cc_final: 0.7848 (pp) REVERT: B 780 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8132 (mt-10) REVERT: B 900 MET cc_start: 0.7053 (ptp) cc_final: 0.6582 (ptt) REVERT: B 952 GLU cc_start: 0.7931 (mp0) cc_final: 0.7492 (tp30) REVERT: B 1077 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7660 (tm-30) REVERT: B 1099 TYR cc_start: 0.7864 (m-80) cc_final: 0.7586 (m-80) outliers start: 59 outliers final: 20 residues processed: 327 average time/residue: 1.0854 time to fit residues: 415.3762 Evaluate side-chains 272 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 842 THR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 152 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 231 optimal weight: 0.3980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 303 HIS A 450 HIS A 534 ASN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN A1133 HIS A1135 GLN B 127 HIS B 362 GLN B 623 ASN B 760 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114954 restraints weight = 24016.075| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.86 r_work: 0.3223 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20778 Z= 0.244 Angle : 0.610 9.756 28141 Z= 0.327 Chirality : 0.047 0.198 3141 Planarity : 0.004 0.101 3624 Dihedral : 5.894 58.071 2741 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 3.68 % Allowed : 13.64 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.16), residues: 2526 helix: -0.50 (0.19), residues: 636 sheet: -1.85 (0.21), residues: 505 loop : -1.64 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 629 HIS 0.004 0.001 HIS A 893 PHE 0.023 0.002 PHE B 438 TYR 0.023 0.002 TYR A1108 ARG 0.005 0.001 ARG A 383 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 694) hydrogen bonds : angle 5.42878 ( 1947) SS BOND : bond 0.00253 ( 1) SS BOND : angle 2.24945 ( 2) covalent geometry : bond 0.00588 (20777) covalent geometry : angle 0.61003 (28139) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 270 time to evaluate : 2.444 Fit side-chains REVERT: A 6 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8264 (mmt) REVERT: A 10 ASN cc_start: 0.8417 (m110) cc_final: 0.8119 (m-40) REVERT: A 46 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: A 48 ARG cc_start: 0.6926 (ptp-110) cc_final: 0.6174 (ptp-110) REVERT: A 83 MET cc_start: 0.7419 (mpt) cc_final: 0.7128 (mmt) REVERT: A 135 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7684 (tp30) REVERT: A 447 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8406 (pt) REVERT: A 471 GLN cc_start: 0.7941 (pp30) cc_final: 0.7614 (pp30) REVERT: A 530 ARG cc_start: 0.7483 (mtt90) cc_final: 0.7063 (mtm110) REVERT: A 554 ASP cc_start: 0.8573 (t70) cc_final: 0.8347 (t0) REVERT: A 576 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6704 (tm) REVERT: A 615 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7382 (pt0) REVERT: A 639 ASN cc_start: 0.8511 (m-40) cc_final: 0.8227 (m-40) REVERT: A 653 ASP cc_start: 0.6830 (m-30) cc_final: 0.5976 (t0) REVERT: A 711 TYR cc_start: 0.7271 (t80) cc_final: 0.7048 (t80) REVERT: A 808 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7937 (mtp) REVERT: A 834 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7912 (tptt) REVERT: A 868 TYR cc_start: 0.8305 (t80) cc_final: 0.7783 (t80) REVERT: A 876 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8390 (mtm110) REVERT: A 971 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7962 (tttm) REVERT: A 1209 MET cc_start: 0.5677 (ptt) cc_final: 0.4218 (tmm) REVERT: A 1276 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 11 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7678 (ttp-170) REVERT: B 94 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: B 207 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7884 (mtm-85) REVERT: B 239 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7201 (tt) REVERT: B 253 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7746 (tttm) REVERT: B 274 GLN cc_start: 0.8459 (mt0) cc_final: 0.8146 (mt0) REVERT: B 425 GLU cc_start: 0.7421 (mp0) cc_final: 0.6910 (mp0) REVERT: B 452 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7562 (mmt) REVERT: B 479 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7006 (pp20) REVERT: B 520 ASP cc_start: 0.8314 (m-30) cc_final: 0.7974 (m-30) REVERT: B 627 MET cc_start: 0.9141 (mtm) cc_final: 0.8778 (mtp) REVERT: B 648 ILE cc_start: 0.8288 (pt) cc_final: 0.7833 (pp) REVERT: B 780 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 845 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6696 (m-30) REVERT: B 900 MET cc_start: 0.7297 (ptp) cc_final: 0.6841 (ptt) REVERT: B 952 GLU cc_start: 0.7927 (mp0) cc_final: 0.7563 (tp30) REVERT: B 1099 TYR cc_start: 0.7884 (m-80) cc_final: 0.7613 (m-80) REVERT: B 1121 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7184 (tttp) REVERT: B 1170 VAL cc_start: 0.4826 (OUTLIER) cc_final: 0.4588 (m) outliers start: 84 outliers final: 30 residues processed: 316 average time/residue: 1.0670 time to fit residues: 396.9149 Evaluate side-chains 293 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain B residue 1170 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 225 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 227 optimal weight: 0.8980 chunk 158 optimal weight: 0.0030 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 619 GLN A 860 ASN A 980 ASN A1067 ASN B 127 HIS B1059 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121141 restraints weight = 23903.150| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.82 r_work: 0.3328 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 20778 Z= 0.107 Angle : 0.497 8.444 28141 Z= 0.269 Chirality : 0.043 0.159 3141 Planarity : 0.004 0.099 3624 Dihedral : 5.338 58.220 2741 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 2.89 % Allowed : 15.70 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2526 helix: 0.34 (0.21), residues: 636 sheet: -1.66 (0.23), residues: 480 loop : -1.42 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 629 HIS 0.004 0.001 HIS A 922 PHE 0.019 0.001 PHE B 438 TYR 0.017 0.001 TYR B 576 ARG 0.003 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 694) hydrogen bonds : angle 4.92395 ( 1947) SS BOND : bond 0.00034 ( 1) SS BOND : angle 1.73661 ( 2) covalent geometry : bond 0.00246 (20777) covalent geometry : angle 0.49708 (28139) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 289 time to evaluate : 2.477 Fit side-chains REVERT: A 6 MET cc_start: 0.8743 (mtp) cc_final: 0.8362 (mmt) REVERT: A 10 ASN cc_start: 0.8242 (m110) cc_final: 0.7942 (m-40) REVERT: A 48 ARG cc_start: 0.6939 (ptp-110) cc_final: 0.6169 (ptp-110) REVERT: A 83 MET cc_start: 0.7244 (mpt) cc_final: 0.6989 (mmt) REVERT: A 135 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: A 383 ARG cc_start: 0.7517 (ttt-90) cc_final: 0.7276 (ttt90) REVERT: A 447 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8143 (pt) REVERT: A 471 GLN cc_start: 0.7947 (pp30) cc_final: 0.7548 (pp30) REVERT: A 528 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7435 (mtp) REVERT: A 530 ARG cc_start: 0.7431 (mtt90) cc_final: 0.7050 (mtm110) REVERT: A 576 LEU cc_start: 0.7009 (pt) cc_final: 0.6609 (tm) REVERT: A 615 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7355 (pt0) REVERT: A 639 ASN cc_start: 0.8393 (m-40) cc_final: 0.8141 (m-40) REVERT: A 653 ASP cc_start: 0.6648 (m-30) cc_final: 0.5866 (t0) REVERT: A 711 TYR cc_start: 0.7311 (t80) cc_final: 0.7076 (OUTLIER) REVERT: A 776 MET cc_start: 0.8029 (mtp) cc_final: 0.7800 (mtm) REVERT: A 834 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7945 (tptt) REVERT: A 866 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7515 (tm-30) REVERT: A 868 TYR cc_start: 0.8193 (t80) cc_final: 0.7580 (t80) REVERT: A 876 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8347 (mtm110) REVERT: A 971 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8012 (tttm) REVERT: A 1139 ASP cc_start: 0.8223 (m-30) cc_final: 0.7962 (m-30) REVERT: A 1209 MET cc_start: 0.5786 (ptt) cc_final: 0.4337 (tmm) REVERT: A 1276 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8196 (p) REVERT: A 1288 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7487 (tttp) REVERT: A 1321 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7106 (tp30) REVERT: B 11 ARG cc_start: 0.8020 (ttm170) cc_final: 0.7686 (ttp-170) REVERT: B 94 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7517 (mp0) REVERT: B 135 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8443 (mp) REVERT: B 175 ILE cc_start: 0.8762 (mp) cc_final: 0.8525 (mp) REVERT: B 207 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7858 (mtm-85) REVERT: B 274 GLN cc_start: 0.8381 (mt0) cc_final: 0.8075 (mt0) REVERT: B 344 ASN cc_start: 0.8492 (t0) cc_final: 0.8262 (t0) REVERT: B 425 GLU cc_start: 0.7471 (mp0) cc_final: 0.7047 (mp0) REVERT: B 445 GLN cc_start: 0.8486 (pt0) cc_final: 0.8020 (pt0) REVERT: B 452 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7488 (mmt) REVERT: B 479 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6983 (pp20) REVERT: B 520 ASP cc_start: 0.8257 (m-30) cc_final: 0.7908 (m-30) REVERT: B 627 MET cc_start: 0.9067 (mtm) cc_final: 0.8850 (mtp) REVERT: B 780 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 845 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6466 (m-30) REVERT: B 847 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: B 858 GLN cc_start: 0.8539 (tt0) cc_final: 0.8206 (pt0) REVERT: B 900 MET cc_start: 0.6860 (ptp) cc_final: 0.6396 (ptt) REVERT: B 952 GLU cc_start: 0.7883 (mp0) cc_final: 0.7605 (tp30) REVERT: B 1121 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7235 (tttp) REVERT: B 1170 VAL cc_start: 0.4803 (OUTLIER) cc_final: 0.4579 (m) outliers start: 66 outliers final: 20 residues processed: 324 average time/residue: 1.0244 time to fit residues: 390.1856 Evaluate side-chains 288 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 926 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1121 LYS Chi-restraints excluded: chain B residue 1170 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 173 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN B 646 GLN B1059 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116511 restraints weight = 24110.234| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.88 r_work: 0.3242 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20778 Z= 0.199 Angle : 0.563 8.334 28141 Z= 0.299 Chirality : 0.045 0.214 3141 Planarity : 0.004 0.098 3624 Dihedral : 5.262 51.590 2737 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 3.38 % Allowed : 16.71 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.16), residues: 2526 helix: 0.46 (0.21), residues: 638 sheet: -1.63 (0.22), residues: 506 loop : -1.38 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 629 HIS 0.012 0.001 HIS B 127 PHE 0.021 0.002 PHE B 438 TYR 0.021 0.002 TYR A1108 ARG 0.003 0.000 ARG A1144 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 694) hydrogen bonds : angle 4.99922 ( 1947) SS BOND : bond 0.00264 ( 1) SS BOND : angle 1.93753 ( 2) covalent geometry : bond 0.00480 (20777) covalent geometry : angle 0.56280 (28139) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 262 time to evaluate : 2.322 Fit side-chains REVERT: A 6 MET cc_start: 0.8787 (mtp) cc_final: 0.8503 (mmt) REVERT: A 10 ASN cc_start: 0.8307 (m110) cc_final: 0.8004 (m-40) REVERT: A 46 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: A 48 ARG cc_start: 0.6902 (ptp-110) cc_final: 0.6160 (ptp-110) REVERT: A 135 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7740 (tp30) REVERT: A 295 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: A 447 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8229 (pt) REVERT: A 471 GLN cc_start: 0.7985 (pp30) cc_final: 0.7511 (pp30) REVERT: A 528 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7461 (mtp) REVERT: A 530 ARG cc_start: 0.7466 (mtt90) cc_final: 0.7010 (mtm110) REVERT: A 576 LEU cc_start: 0.7042 (pt) cc_final: 0.6630 (tm) REVERT: A 608 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8139 (m) REVERT: A 615 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7477 (pt0) REVERT: A 639 ASN cc_start: 0.8447 (m-40) cc_final: 0.8175 (m-40) REVERT: A 647 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8529 (p) REVERT: A 653 ASP cc_start: 0.6795 (m-30) cc_final: 0.5909 (t0) REVERT: A 711 TYR cc_start: 0.7358 (t80) cc_final: 0.7125 (t80) REVERT: A 776 MET cc_start: 0.8098 (mtp) cc_final: 0.7819 (mtm) REVERT: A 834 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7887 (tptt) REVERT: A 868 TYR cc_start: 0.8233 (t80) cc_final: 0.7636 (t80) REVERT: A 876 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8356 (mtm110) REVERT: A 971 LYS cc_start: 0.8461 (ttmt) cc_final: 0.7990 (tttm) REVERT: A 1025 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: A 1209 MET cc_start: 0.5843 (ptt) cc_final: 0.4327 (tmm) REVERT: A 1276 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8226 (p) REVERT: A 1288 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7454 (tttp) REVERT: A 1321 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7149 (tp30) REVERT: B 11 ARG cc_start: 0.8034 (ttm170) cc_final: 0.7675 (ttp-170) REVERT: B 94 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: B 135 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 253 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7713 (tttm) REVERT: B 271 GLU cc_start: 0.7751 (mp0) cc_final: 0.7432 (mp0) REVERT: B 274 GLN cc_start: 0.8410 (mt0) cc_final: 0.8078 (mt0) REVERT: B 344 ASN cc_start: 0.8431 (t0) cc_final: 0.8143 (t0) REVERT: B 425 GLU cc_start: 0.7465 (mp0) cc_final: 0.6879 (mp0) REVERT: B 452 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7535 (mmt) REVERT: B 487 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: B 520 ASP cc_start: 0.8319 (m-30) cc_final: 0.8014 (m-30) REVERT: B 627 MET cc_start: 0.9105 (mtm) cc_final: 0.8890 (mtp) REVERT: B 648 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7753 (pp) REVERT: B 780 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 845 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: B 858 GLN cc_start: 0.8641 (tt0) cc_final: 0.8172 (pt0) REVERT: B 900 MET cc_start: 0.7111 (ptp) cc_final: 0.6653 (ptt) REVERT: B 952 GLU cc_start: 0.7956 (mp0) cc_final: 0.7587 (tp30) outliers start: 77 outliers final: 31 residues processed: 311 average time/residue: 1.0385 time to fit residues: 379.3942 Evaluate side-chains 297 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 251 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 242 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN B1059 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.120998 restraints weight = 23829.679| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.81 r_work: 0.3302 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20778 Z= 0.113 Angle : 0.499 7.442 28141 Z= 0.268 Chirality : 0.043 0.163 3141 Planarity : 0.003 0.096 3624 Dihedral : 4.943 38.746 2737 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 3.29 % Allowed : 17.41 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2526 helix: 0.80 (0.21), residues: 638 sheet: -1.50 (0.22), residues: 507 loop : -1.26 (0.16), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 629 HIS 0.005 0.001 HIS A 922 PHE 0.018 0.001 PHE B 438 TYR 0.018 0.001 TYR A1291 ARG 0.003 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 694) hydrogen bonds : angle 4.76703 ( 1947) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.63849 ( 2) covalent geometry : bond 0.00263 (20777) covalent geometry : angle 0.49865 (28139) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 283 time to evaluate : 2.211 Fit side-chains REVERT: A 48 ARG cc_start: 0.6912 (ptp-110) cc_final: 0.6080 (ptp-110) REVERT: A 135 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: A 295 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: A 329 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 471 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7516 (pp30) REVERT: A 528 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7443 (mtp) REVERT: A 530 ARG cc_start: 0.7424 (mtt90) cc_final: 0.7018 (mtm110) REVERT: A 576 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6517 (tm) REVERT: A 615 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7518 (pt0) REVERT: A 639 ASN cc_start: 0.8346 (m-40) cc_final: 0.8088 (m-40) REVERT: A 653 ASP cc_start: 0.6571 (m-30) cc_final: 0.5773 (t0) REVERT: A 711 TYR cc_start: 0.7337 (t80) cc_final: 0.7127 (t80) REVERT: A 776 MET cc_start: 0.8004 (mtp) cc_final: 0.7783 (mtm) REVERT: A 834 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7874 (tptt) REVERT: A 868 TYR cc_start: 0.8164 (t80) cc_final: 0.7585 (t80) REVERT: A 876 ARG cc_start: 0.8623 (ttp-110) cc_final: 0.8339 (mtm110) REVERT: A 971 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8030 (tttm) REVERT: A 1025 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: A 1139 ASP cc_start: 0.8232 (m-30) cc_final: 0.8008 (m-30) REVERT: A 1209 MET cc_start: 0.5760 (ptt) cc_final: 0.4341 (tmm) REVERT: A 1276 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 1288 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7410 (tttp) REVERT: B 11 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7590 (ttp-170) REVERT: B 94 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7330 (mp0) REVERT: B 135 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8433 (mp) REVERT: B 156 ASN cc_start: 0.8069 (t0) cc_final: 0.7736 (t0) REVERT: B 253 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7706 (tttm) REVERT: B 267 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7065 (ttpp) REVERT: B 271 GLU cc_start: 0.7688 (mp0) cc_final: 0.7379 (mp0) REVERT: B 274 GLN cc_start: 0.8355 (mt0) cc_final: 0.8004 (mt0) REVERT: B 344 ASN cc_start: 0.8397 (t0) cc_final: 0.8095 (t0) REVERT: B 425 GLU cc_start: 0.7472 (mp0) cc_final: 0.7015 (mp0) REVERT: B 452 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7507 (mmt) REVERT: B 520 ASP cc_start: 0.8298 (m-30) cc_final: 0.7978 (m-30) REVERT: B 648 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7592 (pp) REVERT: B 780 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 845 ASP cc_start: 0.6723 (OUTLIER) cc_final: 0.6435 (m-30) REVERT: B 847 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7678 (mp0) REVERT: B 858 GLN cc_start: 0.8538 (tt0) cc_final: 0.8285 (pt0) REVERT: B 900 MET cc_start: 0.6857 (ptp) cc_final: 0.6396 (ptt) REVERT: B 952 GLU cc_start: 0.7937 (mp0) cc_final: 0.7577 (tp30) REVERT: B 954 ASN cc_start: 0.8530 (m-40) cc_final: 0.8259 (m110) REVERT: B 1077 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7822 (tp40) outliers start: 75 outliers final: 33 residues processed: 328 average time/residue: 0.9512 time to fit residues: 369.2270 Evaluate side-chains 307 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 229 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN A1079 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.146827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119946 restraints weight = 23864.577| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.81 r_work: 0.3293 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20778 Z= 0.135 Angle : 0.520 11.463 28141 Z= 0.276 Chirality : 0.044 0.263 3141 Planarity : 0.003 0.094 3624 Dihedral : 4.898 33.533 2737 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.70 % Rotamer: Outliers : 2.94 % Allowed : 18.68 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2526 helix: 0.86 (0.21), residues: 643 sheet: -1.45 (0.23), residues: 497 loop : -1.21 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 629 HIS 0.004 0.001 HIS A 922 PHE 0.018 0.001 PHE B 438 TYR 0.021 0.001 TYR A 518 ARG 0.006 0.000 ARG A 901 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 694) hydrogen bonds : angle 4.72467 ( 1947) SS BOND : bond 0.00165 ( 1) SS BOND : angle 1.69467 ( 2) covalent geometry : bond 0.00324 (20777) covalent geometry : angle 0.51973 (28139) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 268 time to evaluate : 2.324 Fit side-chains REVERT: A 135 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: A 295 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: A 447 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8046 (pt) REVERT: A 471 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7540 (pp30) REVERT: A 528 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7436 (mtp) REVERT: A 530 ARG cc_start: 0.7446 (mtt90) cc_final: 0.7006 (mtm110) REVERT: A 615 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7513 (pt0) REVERT: A 639 ASN cc_start: 0.8344 (m-40) cc_final: 0.8090 (m-40) REVERT: A 653 ASP cc_start: 0.6572 (m-30) cc_final: 0.5797 (t0) REVERT: A 776 MET cc_start: 0.8051 (mtp) cc_final: 0.7800 (mtm) REVERT: A 834 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7856 (tptt) REVERT: A 868 TYR cc_start: 0.8209 (t80) cc_final: 0.7642 (t80) REVERT: A 876 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8338 (mtm110) REVERT: A 971 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8008 (tttm) REVERT: A 1025 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: A 1045 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7211 (ttp-110) REVERT: A 1139 ASP cc_start: 0.8255 (m-30) cc_final: 0.8027 (m-30) REVERT: A 1209 MET cc_start: 0.5748 (ptt) cc_final: 0.4324 (tmm) REVERT: A 1276 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8241 (p) REVERT: A 1288 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7425 (tttp) REVERT: B 94 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: B 135 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8452 (mp) REVERT: B 253 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7692 (tttm) REVERT: B 267 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7063 (ttpp) REVERT: B 271 GLU cc_start: 0.7695 (mp0) cc_final: 0.7391 (mp0) REVERT: B 274 GLN cc_start: 0.8357 (mt0) cc_final: 0.8020 (mt0) REVERT: B 344 ASN cc_start: 0.8451 (t0) cc_final: 0.8167 (t0) REVERT: B 425 GLU cc_start: 0.7451 (mp0) cc_final: 0.6983 (mp0) REVERT: B 452 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7509 (mmt) REVERT: B 648 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7523 (pp) REVERT: B 780 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8043 (mt-10) REVERT: B 845 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.6399 (m-30) REVERT: B 847 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7661 (mp0) REVERT: B 858 GLN cc_start: 0.8554 (tt0) cc_final: 0.8291 (pt0) REVERT: B 900 MET cc_start: 0.6866 (ptp) cc_final: 0.6419 (ptt) REVERT: B 952 GLU cc_start: 0.7932 (mp0) cc_final: 0.7551 (tp30) REVERT: B 954 ASN cc_start: 0.8543 (m-40) cc_final: 0.8246 (m110) outliers start: 67 outliers final: 33 residues processed: 306 average time/residue: 1.0771 time to fit residues: 387.5468 Evaluate side-chains 304 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1045 ARG Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 146 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 175 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN A1067 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119544 restraints weight = 24034.223| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.81 r_work: 0.3302 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20778 Z= 0.147 Angle : 0.527 9.971 28141 Z= 0.280 Chirality : 0.044 0.210 3141 Planarity : 0.003 0.093 3624 Dihedral : 4.906 33.955 2737 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 2.89 % Allowed : 19.21 % Favored : 77.89 % 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: -1.03 (0.17), residues: 2526 helix: 0.92 (0.21), residues: 643 sheet: -1.42 (0.23), residues: 496 loop : -1.16 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 629 HIS 0.004 0.001 HIS A 922 PHE 0.018 0.001 PHE B 438 TYR 0.020 0.001 TYR A 518 ARG 0.006 0.000 ARG A 901 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 694) hydrogen bonds : angle 4.73488 ( 1947) SS BOND : bond 0.00222 ( 1) SS BOND : angle 1.71592 ( 2) covalent geometry : bond 0.00353 (20777) covalent geometry : angle 0.52694 (28139) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 262 time to evaluate : 2.363 Fit side-chains REVERT: A 10 ASN cc_start: 0.8304 (m110) cc_final: 0.8055 (m-40) REVERT: A 48 ARG cc_start: 0.6876 (ptp-110) cc_final: 0.6113 (ptp-110) REVERT: A 135 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7648 (tp30) REVERT: A 295 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: A 447 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8047 (pt) REVERT: A 471 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7507 (pp30) REVERT: A 528 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7405 (mtp) REVERT: A 530 ARG cc_start: 0.7473 (mtt90) cc_final: 0.7065 (mtm110) REVERT: A 615 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7553 (pt0) REVERT: A 639 ASN cc_start: 0.8355 (m-40) cc_final: 0.8095 (m-40) REVERT: A 653 ASP cc_start: 0.6630 (m-30) cc_final: 0.5866 (t0) REVERT: A 776 MET cc_start: 0.8079 (mtp) cc_final: 0.7824 (mtm) REVERT: A 834 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7892 (tptt) REVERT: A 868 TYR cc_start: 0.8249 (t80) cc_final: 0.7662 (t80) REVERT: A 876 ARG cc_start: 0.8616 (ttp-110) cc_final: 0.8331 (mtm110) REVERT: A 971 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8048 (tttm) REVERT: A 1025 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: A 1045 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7275 (ttp-110) REVERT: A 1209 MET cc_start: 0.5671 (ptt) cc_final: 0.4451 (tmm) REVERT: A 1276 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8205 (p) REVERT: A 1288 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7431 (tttp) REVERT: B 94 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: B 135 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8472 (mp) REVERT: B 253 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7709 (tttm) REVERT: B 267 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7107 (ttpp) REVERT: B 271 GLU cc_start: 0.7684 (mp0) cc_final: 0.7389 (mp0) REVERT: B 274 GLN cc_start: 0.8433 (mt0) cc_final: 0.8108 (mt0) REVERT: B 344 ASN cc_start: 0.8508 (t0) cc_final: 0.8218 (t0) REVERT: B 425 GLU cc_start: 0.7462 (mp0) cc_final: 0.7086 (mp0) REVERT: B 452 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7493 (mmt) REVERT: B 780 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8047 (mt-10) REVERT: B 845 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6415 (m-30) REVERT: B 847 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: B 858 GLN cc_start: 0.8563 (tt0) cc_final: 0.8308 (pt0) REVERT: B 900 MET cc_start: 0.6915 (ptp) cc_final: 0.6484 (ptt) REVERT: B 952 GLU cc_start: 0.7965 (mp0) cc_final: 0.7643 (tp30) REVERT: B 954 ASN cc_start: 0.8588 (m-40) cc_final: 0.8337 (m110) outliers start: 66 outliers final: 32 residues processed: 304 average time/residue: 0.9862 time to fit residues: 354.5831 Evaluate side-chains 297 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1045 ARG Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 102 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 952 GLN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117899 restraints weight = 23969.336| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.84 r_work: 0.3257 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 0.064 20778 Z= 0.176 Angle : 0.557 9.576 28141 Z= 0.294 Chirality : 0.045 0.216 3141 Planarity : 0.004 0.091 3624 Dihedral : 5.015 35.063 2737 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 2.81 % Allowed : 19.69 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2526 helix: 0.91 (0.21), residues: 640 sheet: -1.44 (0.23), residues: 496 loop : -1.16 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 629 HIS 0.004 0.001 HIS A 893 PHE 0.019 0.002 PHE B 438 TYR 0.021 0.002 TYR A 518 ARG 0.007 0.000 ARG A 901 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 694) hydrogen bonds : angle 4.80429 ( 1947) SS BOND : bond 0.00271 ( 1) SS BOND : angle 1.75270 ( 2) covalent geometry : bond 0.00423 (20777) covalent geometry : angle 0.55698 (28139) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 248 time to evaluate : 2.289 Fit side-chains REVERT: A 10 ASN cc_start: 0.8330 (m110) cc_final: 0.8073 (m-40) REVERT: A 48 ARG cc_start: 0.6915 (ptp-110) cc_final: 0.6111 (ptp-110) REVERT: A 135 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7724 (tp30) REVERT: A 295 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: A 447 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8119 (pt) REVERT: A 471 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7486 (pp30) REVERT: A 528 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7421 (mtp) REVERT: A 530 ARG cc_start: 0.7442 (mtt90) cc_final: 0.6988 (mtm110) REVERT: A 615 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7506 (pt0) REVERT: A 639 ASN cc_start: 0.8393 (m-40) cc_final: 0.8121 (m-40) REVERT: A 653 ASP cc_start: 0.6675 (m-30) cc_final: 0.5847 (t0) REVERT: A 776 MET cc_start: 0.8196 (mtp) cc_final: 0.7951 (mtm) REVERT: A 834 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7878 (tptt) REVERT: A 868 TYR cc_start: 0.8218 (t80) cc_final: 0.7624 (t80) REVERT: A 876 ARG cc_start: 0.8609 (ttp-110) cc_final: 0.8328 (mtm110) REVERT: A 971 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8029 (tttm) REVERT: A 1025 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: A 1045 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7291 (ttp-110) REVERT: A 1209 MET cc_start: 0.5656 (ptt) cc_final: 0.4495 (tmm) REVERT: A 1225 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8076 (mp0) REVERT: A 1276 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 1288 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7417 (tttp) REVERT: B 42 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6763 (mpp) REVERT: B 94 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: B 135 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8490 (mp) REVERT: B 240 GLN cc_start: 0.8025 (mt0) cc_final: 0.7783 (mt0) REVERT: B 253 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7692 (tttm) REVERT: B 267 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7076 (ttpp) REVERT: B 271 GLU cc_start: 0.7695 (mp0) cc_final: 0.7386 (mp0) REVERT: B 274 GLN cc_start: 0.8423 (mt0) cc_final: 0.8078 (mt0) REVERT: B 344 ASN cc_start: 0.8499 (t0) cc_final: 0.8292 (t0) REVERT: B 425 GLU cc_start: 0.7389 (mp0) cc_final: 0.6830 (mp0) REVERT: B 452 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7472 (mmt) REVERT: B 780 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 845 ASP cc_start: 0.6820 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: B 847 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: B 858 GLN cc_start: 0.8572 (tt0) cc_final: 0.8298 (pt0) REVERT: B 900 MET cc_start: 0.7052 (ptp) cc_final: 0.6613 (ptt) REVERT: B 952 GLU cc_start: 0.7968 (mp0) cc_final: 0.7591 (tp30) REVERT: B 954 ASN cc_start: 0.8536 (m-40) cc_final: 0.8264 (m110) REVERT: B 1092 ASP cc_start: 0.7539 (m-30) cc_final: 0.7249 (t70) outliers start: 64 outliers final: 36 residues processed: 289 average time/residue: 1.0630 time to fit residues: 361.1876 Evaluate side-chains 295 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1045 ARG Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1321 GLU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1086 SER Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 101 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 33 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 578 ASN A 619 GLN A 952 GLN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120926 restraints weight = 23845.387| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.80 r_work: 0.3299 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20778 Z= 0.128 Angle : 0.529 11.409 28141 Z= 0.280 Chirality : 0.044 0.187 3141 Planarity : 0.003 0.091 3624 Dihedral : 4.858 33.579 2737 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 2.50 % Allowed : 20.31 % Favored : 77.19 % 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: -0.90 (0.17), residues: 2526 helix: 1.11 (0.21), residues: 635 sheet: -1.35 (0.23), residues: 496 loop : -1.10 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 629 HIS 0.005 0.001 HIS A 922 PHE 0.017 0.001 PHE B 438 TYR 0.019 0.001 TYR A 711 ARG 0.006 0.000 ARG A 901 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 694) hydrogen bonds : angle 4.67830 ( 1947) SS BOND : bond 0.00143 ( 1) SS BOND : angle 1.65492 ( 2) covalent geometry : bond 0.00303 (20777) covalent geometry : angle 0.52926 (28139) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 2.240 Fit side-chains REVERT: A 10 ASN cc_start: 0.8272 (m110) cc_final: 0.8023 (m-40) REVERT: A 48 ARG cc_start: 0.6897 (ptp-110) cc_final: 0.6099 (ptp-110) REVERT: A 135 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: A 295 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: A 447 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7970 (pt) REVERT: A 471 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7405 (pp30) REVERT: A 528 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7380 (mtp) REVERT: A 530 ARG cc_start: 0.7443 (mtt90) cc_final: 0.7019 (mtm110) REVERT: A 578 ASN cc_start: 0.5613 (OUTLIER) cc_final: 0.4673 (m-40) REVERT: A 597 LYS cc_start: 0.8731 (mttm) cc_final: 0.8297 (mtpp) REVERT: A 615 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7582 (pt0) REVERT: A 639 ASN cc_start: 0.8309 (m-40) cc_final: 0.8066 (m-40) REVERT: A 653 ASP cc_start: 0.6526 (m-30) cc_final: 0.5782 (t0) REVERT: A 834 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7873 (tptt) REVERT: A 868 TYR cc_start: 0.8188 (t80) cc_final: 0.7589 (t80) REVERT: A 876 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8382 (mtm110) REVERT: A 971 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8029 (tttm) REVERT: A 1025 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7415 (mt-10) REVERT: A 1045 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7230 (ttp-110) REVERT: A 1209 MET cc_start: 0.5592 (ptt) cc_final: 0.4625 (tmt) REVERT: A 1276 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 94 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7524 (mp0) REVERT: B 135 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8425 (mp) REVERT: B 156 ASN cc_start: 0.8056 (t0) cc_final: 0.7743 (t0) REVERT: B 240 GLN cc_start: 0.7940 (mt0) cc_final: 0.7620 (mt0) REVERT: B 253 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7666 (tttm) REVERT: B 267 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7121 (ttpp) REVERT: B 271 GLU cc_start: 0.7639 (mp0) cc_final: 0.7353 (mp0) REVERT: B 274 GLN cc_start: 0.8412 (mt0) cc_final: 0.8074 (mt0) REVERT: B 344 ASN cc_start: 0.8470 (t0) cc_final: 0.8178 (t0) REVERT: B 425 GLU cc_start: 0.7410 (mp0) cc_final: 0.6992 (mp0) REVERT: B 452 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7423 (mmt) REVERT: B 780 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8034 (mt-10) REVERT: B 845 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.6399 (m-30) REVERT: B 847 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: B 858 GLN cc_start: 0.8571 (tt0) cc_final: 0.8331 (pt0) REVERT: B 900 MET cc_start: 0.6863 (ptp) cc_final: 0.6432 (ptt) REVERT: B 952 GLU cc_start: 0.7949 (mp0) cc_final: 0.7623 (tp30) REVERT: B 954 ASN cc_start: 0.8542 (m-40) cc_final: 0.8318 (m110) REVERT: B 1092 ASP cc_start: 0.7461 (m-30) cc_final: 0.7154 (t70) outliers start: 57 outliers final: 31 residues processed: 310 average time/residue: 0.9540 time to fit residues: 349.3647 Evaluate side-chains 301 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1045 ARG Chi-restraints excluded: chain A residue 1276 THR Chi-restraints excluded: chain A residue 1321 GLU Chi-restraints excluded: chain A residue 1326 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 782 THR Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1086 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 246 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 240 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 952 GLN A1067 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116904 restraints weight = 24120.288| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.84 r_work: 0.3241 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20778 Z= 0.211 Angle : 0.597 13.240 28141 Z= 0.311 Chirality : 0.046 0.263 3141 Planarity : 0.004 0.089 3624 Dihedral : 5.101 35.574 2737 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 2.37 % Allowed : 20.53 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2526 helix: 0.93 (0.21), residues: 634 sheet: -1.38 (0.23), residues: 493 loop : -1.14 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 629 HIS 0.005 0.001 HIS A 893 PHE 0.020 0.002 PHE B 438 TYR 0.021 0.002 TYR A1108 ARG 0.007 0.000 ARG A 901 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 694) hydrogen bonds : angle 4.86129 ( 1947) SS BOND : bond 0.00346 ( 1) SS BOND : angle 1.85029 ( 2) covalent geometry : bond 0.00512 (20777) covalent geometry : angle 0.59640 (28139) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13546.01 seconds wall clock time: 234 minutes 48.54 seconds (14088.54 seconds total)