Starting phenix.real_space_refine on Sun Aug 24 14:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c8g_16475/08_2025/8c8g_16475.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c8g_16475/08_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_16475/08_2025/8c8g_16475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c8g_16475/08_2025/8c8g_16475.map" model { file = "/net/cci-nas-00/data/ceres_data/8c8g_16475/08_2025/8c8g_16475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c8g_16475/08_2025/8c8g_16475.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.03, per 1000 atoms: 0.20 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: 1.49 Conformation dependent library (CDL) restraints added in 791.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.95 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: 4.64 Time building geometry restraints manager: 1.92 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: 2.250 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.910 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.018 0.002 ARG A 766 TYR 0.050 0.008 TYR A1108 PHE 0.053 0.007 PHE A1099 TRP 0.042 0.009 TRP B 631 HIS 0.035 0.004 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.01284 (20777) covalent geometry : angle 1.49727 (28139) SS BOND : bond 0.03999 ( 1) SS BOND : angle 4.95621 ( 2) hydrogen bonds : bond 0.26048 ( 694) hydrogen bonds : angle 10.97668 ( 1947) *********************** 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 : 0.833 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: 0.7143 (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: 0.5960 time to fit residues: 257.4567 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 : 0.702 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 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 Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119993 restraints weight = 23727.490| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.82 r_work: 0.3270 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 20778 Z= 0.133 Angle : 0.562 10.542 28141 Z= 0.308 Chirality : 0.044 0.155 3141 Planarity : 0.004 0.102 3624 Dihedral : 6.205 56.648 2751 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 2.59 % Allowed : 11.58 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.15), residues: 2526 helix: -1.46 (0.18), residues: 641 sheet: -1.89 (0.22), residues: 485 loop : -1.84 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 553 TYR 0.019 0.001 TYR A1108 PHE 0.024 0.001 PHE B 438 TRP 0.013 0.001 TRP A 629 HIS 0.006 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00304 (20777) covalent geometry : angle 0.56141 (28139) SS BOND : bond 0.00143 ( 1) SS BOND : angle 2.21405 ( 2) hydrogen bonds : bond 0.03874 ( 694) hydrogen bonds : angle 5.71418 ( 1947) *********************** 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 357 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 298 time to evaluate : 0.987 Fit side-chains REVERT: A 10 ASN cc_start: 0.8319 (m110) cc_final: 0.8029 (m-40) REVERT: A 48 ARG cc_start: 0.6777 (ptp-110) cc_final: 0.6059 (ptp-110) REVERT: A 94 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7685 (mtm-85) REVERT: A 447 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8326 (pt) REVERT: A 471 GLN cc_start: 0.7748 (pp30) cc_final: 0.7478 (pp30) REVERT: A 530 ARG cc_start: 0.7380 (mtt90) cc_final: 0.7006 (mtm110) REVERT: A 576 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6721 (tm) REVERT: A 593 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: A 615 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7245 (pt0) REVERT: A 639 ASN cc_start: 0.8512 (m-40) cc_final: 0.8237 (m-40) REVERT: A 653 ASP cc_start: 0.6746 (m-30) cc_final: 0.5848 (t0) REVERT: A 711 TYR cc_start: 0.7176 (t80) cc_final: 0.6905 (t80) REVERT: A 808 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7910 (mtp) REVERT: A 834 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7889 (tttt) REVERT: A 868 TYR cc_start: 0.8185 (t80) cc_final: 0.7598 (t80) REVERT: A 876 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8412 (mtm110) REVERT: A 971 LYS cc_start: 0.8429 (ttmt) cc_final: 0.7929 (tttm) REVERT: A 980 ASN cc_start: 0.7936 (m110) cc_final: 0.7661 (m110) REVERT: A 1209 MET cc_start: 0.5513 (ptt) cc_final: 0.4059 (tmm) REVERT: A 1288 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7419 (tttp) REVERT: B 94 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7697 (mp0) REVERT: B 207 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7853 (mtm-85) REVERT: B 239 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7114 (tt) REVERT: B 253 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7699 (tttm) REVERT: B 274 GLN cc_start: 0.8445 (mt0) cc_final: 0.8149 (mt0) REVERT: B 326 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8377 (mt-10) REVERT: B 425 GLU cc_start: 0.7440 (mp0) cc_final: 0.7043 (mp0) REVERT: B 479 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7120 (pp20) REVERT: B 627 MET cc_start: 0.9117 (mtm) cc_final: 0.8848 (mtp) REVERT: B 648 ILE cc_start: 0.8287 (pt) cc_final: 0.7852 (pp) REVERT: B 780 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8131 (mt-10) REVERT: B 900 MET cc_start: 0.7061 (ptp) cc_final: 0.6588 (ptt) REVERT: B 934 ASP cc_start: 0.8166 (m-30) cc_final: 0.7870 (m-30) REVERT: B 952 GLU cc_start: 0.7912 (mp0) cc_final: 0.7492 (tp30) REVERT: B 1077 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7676 (tm-30) REVERT: B 1099 TYR cc_start: 0.7871 (m-80) cc_final: 0.7597 (m-80) outliers start: 59 outliers final: 20 residues processed: 330 average time/residue: 0.5619 time to fit residues: 215.7877 Evaluate side-chains 274 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 239 LEU 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 169 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 314 HIS A 381 ASN 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 646 GLN B 760 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113569 restraints weight = 24372.810| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.86 r_work: 0.3204 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 20778 Z= 0.296 Angle : 0.649 10.014 28141 Z= 0.346 Chirality : 0.049 0.184 3141 Planarity : 0.004 0.102 3624 Dihedral : 6.093 59.050 2743 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 3.86 % Allowed : 13.77 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.15), residues: 2526 helix: -0.61 (0.19), residues: 637 sheet: -1.89 (0.21), residues: 505 loop : -1.65 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 383 TYR 0.025 0.002 TYR A1108 PHE 0.024 0.002 PHE B 438 TRP 0.018 0.002 TRP A 629 HIS 0.004 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00712 (20777) covalent geometry : angle 0.64903 (28139) SS BOND : bond 0.00342 ( 1) SS BOND : angle 2.36095 ( 2) hydrogen bonds : bond 0.04229 ( 694) hydrogen bonds : angle 5.52280 ( 1947) *********************** 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 347 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 259 time to evaluate : 0.592 Fit side-chains REVERT: A 6 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8316 (mmt) REVERT: A 10 ASN cc_start: 0.8462 (m110) cc_final: 0.8178 (m-40) REVERT: A 46 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: A 48 ARG cc_start: 0.6962 (ptp-110) cc_final: 0.6210 (ptp-110) REVERT: A 135 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7730 (tp30) REVERT: A 447 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8503 (pt) REVERT: A 471 GLN cc_start: 0.7974 (pp30) cc_final: 0.7598 (pp30) REVERT: A 530 ARG cc_start: 0.7490 (mtt90) cc_final: 0.7055 (mtm110) REVERT: A 554 ASP cc_start: 0.8571 (t70) cc_final: 0.8227 (t0) REVERT: A 576 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6689 (tm) REVERT: A 615 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7414 (pt0) REVERT: A 639 ASN cc_start: 0.8509 (m-40) cc_final: 0.8237 (m-40) REVERT: A 653 ASP cc_start: 0.6860 (m-30) cc_final: 0.6050 (t0) REVERT: A 711 TYR cc_start: 0.7286 (t80) cc_final: 0.7083 (t80) REVERT: A 808 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7946 (mtp) REVERT: A 834 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7928 (tptt) REVERT: A 868 TYR cc_start: 0.8342 (t80) cc_final: 0.7819 (t80) REVERT: A 876 ARG cc_start: 0.8650 (ttp-110) cc_final: 0.8394 (mtm110) REVERT: A 971 LYS cc_start: 0.8446 (ttmt) cc_final: 0.7967 (tttm) REVERT: A 1209 MET cc_start: 0.5770 (ptt) cc_final: 0.4292 (tmm) REVERT: A 1276 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8156 (p) REVERT: B 11 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7689 (ttp-170) REVERT: B 94 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: B 207 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7886 (mtm-85) REVERT: B 239 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7238 (tt) REVERT: B 253 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7804 (tttm) REVERT: B 274 GLN cc_start: 0.8473 (mt0) cc_final: 0.8173 (mt0) REVERT: B 326 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8454 (mt-10) REVERT: B 425 GLU cc_start: 0.7326 (mp0) cc_final: 0.6799 (mp0) REVERT: B 452 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7736 (mmt) REVERT: B 479 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7078 (pp20) REVERT: B 520 ASP cc_start: 0.8331 (m-30) cc_final: 0.7979 (m-30) REVERT: B 627 MET cc_start: 0.9156 (mtm) cc_final: 0.8891 (mtp) REVERT: B 780 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8155 (mt-10) REVERT: B 845 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6752 (m-30) REVERT: B 900 MET cc_start: 0.7391 (ptp) cc_final: 0.6926 (ptt) REVERT: B 952 GLU cc_start: 0.7943 (mp0) cc_final: 0.7566 (tp30) REVERT: B 1099 TYR cc_start: 0.7902 (m-80) cc_final: 0.7647 (m-80) REVERT: B 1121 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7182 (tttp) outliers start: 88 outliers final: 34 residues processed: 310 average time/residue: 0.5160 time to fit residues: 185.5433 Evaluate side-chains 284 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 768 MET 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 326 GLU 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 606 LYS 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 848 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 103 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 183 optimal weight: 0.0070 chunk 188 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 243 optimal weight: 0.0770 chunk 106 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 GLN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120811 restraints weight = 23942.629| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.81 r_work: 0.3321 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2206 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 : 0.502 8.661 28141 Z= 0.272 Chirality : 0.043 0.156 3141 Planarity : 0.004 0.100 3624 Dihedral : 5.479 57.023 2743 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 3.16 % Allowed : 15.66 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.16), residues: 2526 helix: 0.28 (0.21), residues: 636 sheet: -1.67 (0.23), residues: 480 loop : -1.43 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.018 0.001 TYR B 576 PHE 0.019 0.001 PHE B 438 TRP 0.015 0.001 TRP A 629 HIS 0.005 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00243 (20777) covalent geometry : angle 0.50145 (28139) SS BOND : bond 0.00029 ( 1) SS BOND : angle 1.77767 ( 2) hydrogen bonds : bond 0.03197 ( 694) hydrogen bonds : angle 4.96225 ( 1947) *********************** 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 352 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 280 time to evaluate : 0.794 Fit side-chains REVERT: A 6 MET cc_start: 0.8752 (mtp) cc_final: 0.8444 (mmt) REVERT: A 10 ASN cc_start: 0.8267 (m110) cc_final: 0.7962 (m-40) REVERT: A 48 ARG cc_start: 0.6948 (ptp-110) cc_final: 0.6180 (ptp-110) REVERT: A 135 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: A 295 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: A 447 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8164 (pt) REVERT: A 471 GLN cc_start: 0.7937 (pp30) cc_final: 0.7505 (pp30) REVERT: A 528 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7437 (mtp) REVERT: A 530 ARG cc_start: 0.7420 (mtt90) cc_final: 0.7044 (mtm110) REVERT: A 554 ASP cc_start: 0.8270 (t70) cc_final: 0.8048 (t0) REVERT: A 576 LEU cc_start: 0.6991 (pt) cc_final: 0.6587 (tm) REVERT: A 615 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7400 (pt0) REVERT: A 639 ASN cc_start: 0.8398 (m-40) cc_final: 0.8136 (m-40) REVERT: A 653 ASP cc_start: 0.6696 (m-30) cc_final: 0.5883 (t0) REVERT: A 711 TYR cc_start: 0.7323 (t80) cc_final: 0.7078 (OUTLIER) REVERT: A 834 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7905 (tptt) REVERT: A 868 TYR cc_start: 0.8208 (t80) cc_final: 0.7598 (t80) REVERT: A 876 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8344 (mtm110) REVERT: A 971 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8019 (tttm) REVERT: A 980 ASN cc_start: 0.7840 (m110) cc_final: 0.7623 (m110) REVERT: A 1139 ASP cc_start: 0.8198 (m-30) cc_final: 0.7945 (m-30) REVERT: A 1209 MET cc_start: 0.5760 (ptt) cc_final: 0.4324 (tmm) REVERT: A 1276 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8225 (p) REVERT: A 1288 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7457 (tttp) REVERT: A 1321 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7100 (tp30) REVERT: B 11 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7693 (ttp-170) REVERT: B 94 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7554 (mp0) REVERT: B 135 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 175 ILE cc_start: 0.8800 (mp) cc_final: 0.8569 (mp) REVERT: B 207 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7806 (mtm-85) REVERT: B 253 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7691 (tttm) REVERT: B 274 GLN cc_start: 0.8380 (mt0) cc_final: 0.8049 (mt0) REVERT: B 344 ASN cc_start: 0.8515 (t0) cc_final: 0.8281 (t0) REVERT: B 425 GLU cc_start: 0.7489 (mp0) cc_final: 0.7065 (mp0) REVERT: B 452 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7464 (mmt) REVERT: B 479 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6962 (pp20) REVERT: B 520 ASP cc_start: 0.8264 (m-30) cc_final: 0.7886 (m-30) REVERT: B 627 MET cc_start: 0.9065 (mtm) cc_final: 0.8853 (mtp) REVERT: B 648 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7736 (pp) REVERT: B 780 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 845 ASP cc_start: 0.6761 (OUTLIER) cc_final: 0.6503 (m-30) REVERT: B 858 GLN cc_start: 0.8617 (tt0) cc_final: 0.8208 (pt0) REVERT: B 900 MET cc_start: 0.6963 (ptp) cc_final: 0.6509 (ptt) REVERT: B 952 GLU cc_start: 0.7898 (mp0) cc_final: 0.7609 (tp30) outliers start: 72 outliers final: 17 residues processed: 319 average time/residue: 0.5235 time to fit residues: 195.5771 Evaluate side-chains 284 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 447 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 135 LEU 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 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 937 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1036 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 136 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 251 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 101 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 249 optimal weight: 30.0000 chunk 134 optimal weight: 6.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN B 127 HIS B 646 GLN B 873 ASN B1059 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113616 restraints weight = 24297.606| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.85 r_work: 0.3182 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 20778 Z= 0.305 Angle : 0.650 8.949 28141 Z= 0.343 Chirality : 0.049 0.233 3141 Planarity : 0.004 0.099 3624 Dihedral : 5.655 55.730 2737 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 3.95 % Allowed : 16.58 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.16), residues: 2526 helix: 0.11 (0.20), residues: 643 sheet: -1.70 (0.22), residues: 507 loop : -1.45 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 553 TYR 0.023 0.002 TYR A1108 PHE 0.023 0.002 PHE B 438 TRP 0.017 0.002 TRP A 629 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00738 (20777) covalent geometry : angle 0.64930 (28139) SS BOND : bond 0.00413 ( 1) SS BOND : angle 2.19212 ( 2) hydrogen bonds : bond 0.03976 ( 694) hydrogen bonds : angle 5.27812 ( 1947) *********************** 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 343 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 253 time to evaluate : 0.959 Fit side-chains REVERT: A 6 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8438 (mmt) REVERT: A 10 ASN cc_start: 0.8463 (m110) cc_final: 0.8168 (m-40) REVERT: A 46 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: A 135 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7830 (tp30) REVERT: A 447 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8405 (pt) REVERT: A 471 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7613 (pp30) REVERT: A 530 ARG cc_start: 0.7504 (mtt90) cc_final: 0.7093 (mtm110) REVERT: A 554 ASP cc_start: 0.8469 (t70) cc_final: 0.8215 (t0) REVERT: A 615 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7471 (pt0) REVERT: A 639 ASN cc_start: 0.8488 (m-40) cc_final: 0.8209 (m-40) REVERT: A 647 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8618 (p) REVERT: A 653 ASP cc_start: 0.6873 (m-30) cc_final: 0.6048 (t0) REVERT: A 711 TYR cc_start: 0.7401 (t80) cc_final: 0.7182 (t80) REVERT: A 834 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7907 (tptt) REVERT: A 868 TYR cc_start: 0.8309 (t80) cc_final: 0.7727 (t80) REVERT: A 876 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8394 (mtm110) REVERT: A 971 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7983 (tttm) REVERT: A 1025 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: A 1209 MET cc_start: 0.5926 (ptt) cc_final: 0.4408 (tmm) REVERT: A 1288 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7456 (tttp) REVERT: B 11 ARG cc_start: 0.8037 (ttm170) cc_final: 0.7699 (ttp-170) REVERT: B 42 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7005 (mpp) REVERT: B 94 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: B 135 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8460 (mp) REVERT: B 239 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7279 (tt) REVERT: B 253 LYS cc_start: 0.8003 (ttmt) cc_final: 0.7791 (tttm) REVERT: B 271 GLU cc_start: 0.7739 (mp0) cc_final: 0.7509 (mp0) REVERT: B 274 GLN cc_start: 0.8436 (mt0) cc_final: 0.8121 (mt0) REVERT: B 425 GLU cc_start: 0.7424 (mp0) cc_final: 0.6846 (mp0) REVERT: B 452 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7730 (mmt) REVERT: B 487 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: B 520 ASP cc_start: 0.8356 (m-30) cc_final: 0.8020 (m-30) REVERT: B 627 MET cc_start: 0.9134 (mtm) cc_final: 0.8884 (mtp) REVERT: B 780 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8173 (mt-10) REVERT: B 845 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: B 858 GLN cc_start: 0.8805 (tt0) cc_final: 0.8330 (tt0) REVERT: B 900 MET cc_start: 0.7360 (ptp) cc_final: 0.6895 (ptt) REVERT: B 952 GLU cc_start: 0.7957 (mp0) cc_final: 0.7597 (tp30) outliers start: 90 outliers final: 34 residues processed: 311 average time/residue: 0.4743 time to fit residues: 172.8806 Evaluate side-chains 281 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 380 VAL 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 523 VAL Chi-restraints excluded: chain A residue 528 MET 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 952 GLN Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain A residue 1083 LEU 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 42 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 127 HIS Chi-restraints excluded: chain B residue 135 LEU 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 441 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 606 LYS 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 730 LEU 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 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 128 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 138 optimal weight: 0.0870 chunk 220 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 218 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 ASN A1079 ASN B 873 ASN B1059 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120902 restraints weight = 23787.165| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.79 r_work: 0.3322 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20778 Z= 0.113 Angle : 0.507 7.957 28141 Z= 0.274 Chirality : 0.043 0.159 3141 Planarity : 0.003 0.097 3624 Dihedral : 5.083 41.398 2737 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 2.76 % Allowed : 18.29 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.16), residues: 2526 helix: 0.68 (0.21), residues: 639 sheet: -1.61 (0.22), residues: 509 loop : -1.27 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 553 TYR 0.019 0.001 TYR A1291 PHE 0.018 0.001 PHE B 438 TRP 0.013 0.001 TRP A 629 HIS 0.013 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00257 (20777) covalent geometry : angle 0.50665 (28139) SS BOND : bond 0.00049 ( 1) SS BOND : angle 1.63923 ( 2) hydrogen bonds : bond 0.03137 ( 694) hydrogen bonds : angle 4.85793 ( 1947) *********************** 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 338 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 0.578 Fit side-chains REVERT: A 6 MET cc_start: 0.8678 (mtp) cc_final: 0.8477 (mmt) REVERT: A 10 ASN cc_start: 0.8281 (m110) cc_final: 0.7988 (m-40) REVERT: A 48 ARG cc_start: 0.6903 (ptp-110) cc_final: 0.6150 (ptp-110) REVERT: A 135 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: A 295 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7468 (tp30) REVERT: A 447 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8115 (pt) REVERT: A 471 GLN cc_start: 0.7956 (pp30) cc_final: 0.7512 (pp30) REVERT: A 528 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7394 (mtp) REVERT: A 530 ARG cc_start: 0.7460 (mtt90) cc_final: 0.7048 (mtm110) REVERT: A 576 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6593 (tm) REVERT: A 615 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7472 (pt0) REVERT: A 639 ASN cc_start: 0.8370 (m-40) cc_final: 0.8122 (m-40) REVERT: A 653 ASP cc_start: 0.6650 (m-30) cc_final: 0.5859 (t0) REVERT: A 834 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7906 (tptt) REVERT: A 866 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 868 TYR cc_start: 0.8189 (t80) cc_final: 0.7673 (t80) REVERT: A 876 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8360 (mtm110) REVERT: A 971 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8030 (tttm) REVERT: A 980 ASN cc_start: 0.7843 (m110) cc_final: 0.7624 (m110) REVERT: A 1139 ASP cc_start: 0.8204 (m-30) cc_final: 0.7956 (m-30) REVERT: A 1209 MET cc_start: 0.5828 (ptt) cc_final: 0.4345 (tmm) REVERT: A 1288 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7422 (tttp) REVERT: B 94 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7456 (mp0) REVERT: B 135 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 253 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7688 (tttm) REVERT: B 271 GLU cc_start: 0.7655 (mp0) cc_final: 0.7376 (mp0) REVERT: B 274 GLN cc_start: 0.8333 (mt0) cc_final: 0.8001 (mt0) REVERT: B 425 GLU cc_start: 0.7469 (mp0) cc_final: 0.6989 (mp0) REVERT: B 452 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7470 (mmt) REVERT: B 520 ASP cc_start: 0.8300 (m-30) cc_final: 0.7953 (m-30) REVERT: B 627 MET cc_start: 0.9034 (mtm) cc_final: 0.8830 (mtp) REVERT: B 648 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 780 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7954 (mt-10) REVERT: B 845 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6497 (m-30) REVERT: B 847 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7651 (mp0) REVERT: B 858 GLN cc_start: 0.8573 (tt0) cc_final: 0.8161 (pt0) REVERT: B 900 MET cc_start: 0.6886 (ptp) cc_final: 0.6446 (ptt) REVERT: B 952 GLU cc_start: 0.7903 (mp0) cc_final: 0.7622 (tp30) REVERT: B 954 ASN cc_start: 0.8566 (m-40) cc_final: 0.8268 (m110) outliers start: 63 outliers final: 20 residues processed: 312 average time/residue: 0.4495 time to fit residues: 165.5743 Evaluate side-chains 283 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU 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 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 926 LEU Chi-restraints excluded: chain A residue 952 GLN 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 135 LEU 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 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 1036 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 145 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 A1079 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 873 ASN B1059 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114722 restraints weight = 24272.569| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.85 r_work: 0.3222 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20778 Z= 0.260 Angle : 0.615 8.631 28141 Z= 0.324 Chirality : 0.048 0.274 3141 Planarity : 0.004 0.095 3624 Dihedral : 5.383 40.880 2737 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.98 % Favored : 93.94 % Rotamer: Outliers : 2.85 % Allowed : 18.95 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.16), residues: 2526 helix: 0.47 (0.21), residues: 643 sheet: -1.74 (0.22), residues: 515 loop : -1.27 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 901 TYR 0.023 0.002 TYR A1108 PHE 0.021 0.002 PHE B 438 TRP 0.017 0.001 TRP A 629 HIS 0.005 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00630 (20777) covalent geometry : angle 0.61474 (28139) SS BOND : bond 0.00359 ( 1) SS BOND : angle 2.03924 ( 2) hydrogen bonds : bond 0.03688 ( 694) hydrogen bonds : angle 5.07734 ( 1947) *********************** 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 315 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 250 time to evaluate : 0.805 Fit side-chains REVERT: A 6 MET cc_start: 0.8744 (mtp) cc_final: 0.8498 (mmt) REVERT: A 10 ASN cc_start: 0.8455 (m110) cc_final: 0.8157 (m-40) REVERT: A 48 ARG cc_start: 0.6885 (ptp-110) cc_final: 0.6125 (ptp-110) REVERT: A 135 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7719 (tp30) REVERT: A 295 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7399 (tp30) REVERT: A 404 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7716 (mt) REVERT: A 447 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8300 (pt) REVERT: A 471 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7600 (pp30) REVERT: A 530 ARG cc_start: 0.7496 (mtt90) cc_final: 0.7068 (mtm110) REVERT: A 615 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7506 (pt0) REVERT: A 639 ASN cc_start: 0.8444 (m-40) cc_final: 0.8153 (m-40) REVERT: A 647 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 653 ASP cc_start: 0.6837 (m-30) cc_final: 0.5945 (t0) REVERT: A 834 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7918 (tptt) REVERT: A 868 TYR cc_start: 0.8301 (t80) cc_final: 0.7771 (t80) REVERT: A 971 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8032 (tttm) REVERT: A 1209 MET cc_start: 0.5890 (ptt) cc_final: 0.4458 (tmm) REVERT: A 1288 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7440 (tttp) REVERT: B 11 ARG cc_start: 0.8022 (ttm170) cc_final: 0.7683 (ttp-170) REVERT: B 42 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7013 (mpp) REVERT: B 94 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 135 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8452 (mp) REVERT: B 253 LYS cc_start: 0.7980 (ttmt) cc_final: 0.7753 (tttm) REVERT: B 271 GLU cc_start: 0.7717 (mp0) cc_final: 0.7358 (mp0) REVERT: B 274 GLN cc_start: 0.8444 (mt0) cc_final: 0.8126 (mt0) REVERT: B 290 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8392 (tt) REVERT: B 425 GLU cc_start: 0.7446 (mp0) cc_final: 0.6910 (mp0) REVERT: B 452 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7578 (mmt) REVERT: B 520 ASP cc_start: 0.8363 (m-30) cc_final: 0.8008 (m-30) REVERT: B 627 MET cc_start: 0.9111 (mtm) cc_final: 0.8860 (mtp) REVERT: B 648 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7818 (pp) REVERT: B 780 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8142 (mt-10) REVERT: B 845 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6765 (m-30) REVERT: B 858 GLN cc_start: 0.8753 (tt0) cc_final: 0.8331 (tt0) REVERT: B 900 MET cc_start: 0.7238 (ptp) cc_final: 0.6792 (ptt) REVERT: B 952 GLU cc_start: 0.7913 (mp0) cc_final: 0.7575 (tp30) outliers start: 65 outliers final: 30 residues processed: 288 average time/residue: 0.5356 time to fit residues: 181.3081 Evaluate side-chains 286 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 516 ILE Chi-restraints excluded: chain A residue 528 MET 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 952 GLN Chi-restraints excluded: chain A residue 1083 LEU 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 42 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 290 ILE 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 514 SER Chi-restraints excluded: chain B residue 646 GLN 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 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 1119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 190 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 183 optimal weight: 0.3980 chunk 76 optimal weight: 0.3980 chunk 88 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 741 ASN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN A1067 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 873 ASN B1059 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121278 restraints weight = 24023.168| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.80 r_work: 0.3326 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20778 Z= 0.112 Angle : 0.510 7.565 28141 Z= 0.274 Chirality : 0.043 0.188 3141 Planarity : 0.003 0.094 3624 Dihedral : 4.942 32.442 2737 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 2.19 % Allowed : 20.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.17), residues: 2526 helix: 0.91 (0.21), residues: 638 sheet: -1.54 (0.22), residues: 495 loop : -1.20 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 901 TYR 0.022 0.001 TYR A 518 PHE 0.017 0.001 PHE B 438 TRP 0.013 0.001 TRP A 629 HIS 0.005 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00259 (20777) covalent geometry : angle 0.50982 (28139) SS BOND : bond 0.00085 ( 1) SS BOND : angle 1.62615 ( 2) hydrogen bonds : bond 0.03060 ( 694) hydrogen bonds : angle 4.76572 ( 1947) *********************** 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 323 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.906 Fit side-chains REVERT: A 10 ASN cc_start: 0.8257 (m110) cc_final: 0.7947 (m-40) REVERT: A 48 ARG cc_start: 0.6924 (ptp-110) cc_final: 0.6097 (ptp-110) REVERT: A 135 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: A 295 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7449 (tp30) REVERT: A 471 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7386 (pp30) REVERT: A 528 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7405 (mtp) REVERT: A 530 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7064 (mtm110) REVERT: A 576 LEU cc_start: 0.6992 (pt) cc_final: 0.6557 (tm) REVERT: A 597 LYS cc_start: 0.8741 (mttm) cc_final: 0.8537 (mttp) REVERT: A 639 ASN cc_start: 0.8323 (m-40) cc_final: 0.8073 (m-40) REVERT: A 653 ASP cc_start: 0.6566 (m-30) cc_final: 0.5808 (t0) REVERT: A 834 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7907 (tptt) REVERT: A 868 TYR cc_start: 0.8203 (t80) cc_final: 0.7664 (t80) REVERT: A 971 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8041 (tttm) REVERT: A 1139 ASP cc_start: 0.8242 (m-30) cc_final: 0.7993 (m-30) REVERT: A 1209 MET cc_start: 0.5892 (ptt) cc_final: 0.4483 (tmm) REVERT: A 1288 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7489 (tttp) REVERT: B 94 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7418 (mp0) REVERT: B 135 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8440 (mp) REVERT: B 156 ASN cc_start: 0.8006 (t0) cc_final: 0.7680 (t0) REVERT: B 240 GLN cc_start: 0.8097 (mt0) cc_final: 0.7878 (mt0) REVERT: B 253 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7680 (tttm) REVERT: B 267 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7119 (ttpp) REVERT: B 271 GLU cc_start: 0.7690 (mp0) cc_final: 0.7401 (mp0) REVERT: B 274 GLN cc_start: 0.8384 (mt0) cc_final: 0.8041 (mt0) REVERT: B 425 GLU cc_start: 0.7457 (mp0) cc_final: 0.7049 (mp0) REVERT: B 452 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7517 (mmt) REVERT: B 520 ASP cc_start: 0.8318 (m-30) cc_final: 0.7947 (m-30) REVERT: B 648 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7553 (pp) REVERT: B 780 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7948 (mt-10) REVERT: B 845 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6428 (m-30) REVERT: B 847 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7593 (mp0) REVERT: B 858 GLN cc_start: 0.8562 (tt0) cc_final: 0.8211 (pt0) REVERT: B 900 MET cc_start: 0.6852 (ptp) cc_final: 0.6409 (ptt) REVERT: B 952 GLU cc_start: 0.7848 (mp0) cc_final: 0.7575 (tp30) REVERT: B 954 ASN cc_start: 0.8527 (m-40) cc_final: 0.8245 (m110) outliers start: 50 outliers final: 28 residues processed: 304 average time/residue: 0.5013 time to fit residues: 180.4187 Evaluate side-chains 293 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 528 MET 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 1002 VAL 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 135 LEU 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 514 SER Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 727 SER 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 926 ILE Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1187 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 178 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117508 restraints weight = 24047.077| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.79 r_work: 0.3279 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20778 Z= 0.186 Angle : 0.567 8.270 28141 Z= 0.300 Chirality : 0.045 0.206 3141 Planarity : 0.004 0.092 3624 Dihedral : 5.098 34.712 2737 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 2.37 % Allowed : 20.26 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.17), residues: 2526 helix: 0.82 (0.21), residues: 643 sheet: -1.55 (0.22), residues: 499 loop : -1.17 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 901 TYR 0.023 0.002 TYR A 518 PHE 0.019 0.002 PHE B 438 TRP 0.015 0.001 TRP A 629 HIS 0.004 0.001 HIS A 893 Details of bonding type rmsd covalent geometry : bond 0.00449 (20777) covalent geometry : angle 0.56638 (28139) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.83730 ( 2) hydrogen bonds : bond 0.03381 ( 694) hydrogen bonds : angle 4.86056 ( 1947) *********************** 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 305 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 0.861 Fit side-chains REVERT: A 10 ASN cc_start: 0.8336 (m110) cc_final: 0.8042 (m-40) REVERT: A 48 ARG cc_start: 0.6904 (ptp-110) cc_final: 0.6113 (ptp-110) REVERT: A 135 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: A 295 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: A 404 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7550 (mt) REVERT: A 471 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7543 (pp30) REVERT: A 528 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7382 (mtp) REVERT: A 530 ARG cc_start: 0.7463 (mtt90) cc_final: 0.7065 (mtm110) REVERT: A 597 LYS cc_start: 0.8798 (mttm) cc_final: 0.8443 (mttm) REVERT: A 639 ASN cc_start: 0.8389 (m-40) cc_final: 0.8108 (m-40) REVERT: A 653 ASP cc_start: 0.6742 (m-30) cc_final: 0.5931 (t0) REVERT: A 834 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7902 (tptt) REVERT: A 868 TYR cc_start: 0.8271 (t80) cc_final: 0.7742 (t80) REVERT: A 952 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: A 971 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8051 (tttm) REVERT: A 1139 ASP cc_start: 0.8343 (m-30) cc_final: 0.8109 (m-30) REVERT: A 1209 MET cc_start: 0.5865 (ptt) cc_final: 0.4580 (tmm) REVERT: A 1288 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7442 (tttp) REVERT: B 42 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7168 (mpp) REVERT: B 94 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7417 (mp0) REVERT: B 135 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 253 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7733 (tttm) REVERT: B 267 LYS cc_start: 0.8043 (ttmm) cc_final: 0.7121 (ttpp) REVERT: B 271 GLU cc_start: 0.7696 (mp0) cc_final: 0.7395 (mp0) REVERT: B 274 GLN cc_start: 0.8458 (mt0) cc_final: 0.8127 (mt0) REVERT: B 425 GLU cc_start: 0.7452 (mp0) cc_final: 0.6939 (mp0) REVERT: B 452 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7538 (mmt) REVERT: B 520 ASP cc_start: 0.8368 (m-30) cc_final: 0.8081 (m-30) REVERT: B 780 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 845 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6509 (m-30) REVERT: B 858 GLN cc_start: 0.8636 (tt0) cc_final: 0.8236 (pt0) REVERT: B 900 MET cc_start: 0.7063 (ptp) cc_final: 0.6622 (ptt) REVERT: B 952 GLU cc_start: 0.7884 (mp0) cc_final: 0.7648 (tp30) REVERT: B 954 ASN cc_start: 0.8522 (m-40) cc_final: 0.8292 (m110) outliers start: 54 outliers final: 31 residues processed: 284 average time/residue: 0.5262 time to fit residues: 175.9395 Evaluate side-chains 285 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 528 MET 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 880 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 952 GLN Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1083 LEU 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 42 MET 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 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 727 SER 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 937 SER Chi-restraints excluded: chain B residue 1026 MET Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1119 THR Chi-restraints excluded: chain B residue 1187 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 162 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 161 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 741 ASN A 952 GLN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN A1067 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1059 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117467 restraints weight = 24167.877| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.80 r_work: 0.3279 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20778 Z= 0.184 Angle : 0.569 8.184 28141 Z= 0.300 Chirality : 0.045 0.197 3141 Planarity : 0.004 0.091 3624 Dihedral : 5.144 34.977 2737 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 2.37 % Allowed : 20.57 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.17), residues: 2526 helix: 0.85 (0.21), residues: 640 sheet: -1.54 (0.22), residues: 502 loop : -1.15 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 901 TYR 0.021 0.002 TYR A 711 PHE 0.019 0.002 PHE B 438 TRP 0.015 0.001 TRP A 629 HIS 0.004 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00444 (20777) covalent geometry : angle 0.56919 (28139) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.80870 ( 2) hydrogen bonds : bond 0.03385 ( 694) hydrogen bonds : angle 4.87191 ( 1947) ********************** 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 297 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 0.842 Fit side-chains REVERT: A 10 ASN cc_start: 0.8374 (m110) cc_final: 0.8088 (m-40) REVERT: A 46 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: A 48 ARG cc_start: 0.6880 (ptp-110) cc_final: 0.6126 (ptp-110) REVERT: A 135 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: A 295 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: A 404 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7517 (mt) REVERT: A 471 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7554 (pp30) REVERT: A 528 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7394 (mtp) REVERT: A 530 ARG cc_start: 0.7441 (mtt90) cc_final: 0.7053 (mtm110) REVERT: A 576 LEU cc_start: 0.7054 (pt) cc_final: 0.6847 (tm) REVERT: A 578 ASN cc_start: 0.5765 (OUTLIER) cc_final: 0.4805 (m-40) REVERT: A 597 LYS cc_start: 0.8787 (mttm) cc_final: 0.8473 (mttm) REVERT: A 639 ASN cc_start: 0.8370 (m-40) cc_final: 0.8104 (m-40) REVERT: A 653 ASP cc_start: 0.6736 (m-30) cc_final: 0.5915 (t0) REVERT: A 834 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7928 (tptt) REVERT: A 868 TYR cc_start: 0.8262 (t80) cc_final: 0.7724 (t80) REVERT: A 971 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8071 (tttm) REVERT: A 1139 ASP cc_start: 0.8337 (m-30) cc_final: 0.8079 (m-30) REVERT: A 1209 MET cc_start: 0.5768 (ptt) cc_final: 0.4580 (tmm) REVERT: A 1288 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7443 (tttp) REVERT: B 42 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7167 (mpp) REVERT: B 94 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7430 (mp0) REVERT: B 135 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8485 (mp) REVERT: B 253 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7714 (tttm) REVERT: B 267 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7112 (ttpp) REVERT: B 271 GLU cc_start: 0.7690 (mp0) cc_final: 0.7388 (mp0) REVERT: B 274 GLN cc_start: 0.8446 (mt0) cc_final: 0.8115 (mt0) REVERT: B 425 GLU cc_start: 0.7452 (mp0) cc_final: 0.6905 (mp0) REVERT: B 452 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7532 (mmt) REVERT: B 520 ASP cc_start: 0.8358 (m-30) cc_final: 0.8073 (m-30) REVERT: B 780 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 845 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6558 (m-30) REVERT: B 858 GLN cc_start: 0.8643 (tt0) cc_final: 0.8237 (pt0) REVERT: B 900 MET cc_start: 0.7115 (ptp) cc_final: 0.6668 (ptt) REVERT: B 952 GLU cc_start: 0.7917 (mp0) cc_final: 0.7667 (tp30) REVERT: B 954 ASN cc_start: 0.8534 (m-40) cc_final: 0.8307 (m110) outliers start: 54 outliers final: 28 residues processed: 276 average time/residue: 0.5288 time to fit residues: 172.5514 Evaluate side-chains 278 residues out of total 2280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU 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 528 MET Chi-restraints excluded: chain A residue 578 ASN 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 880 VAL Chi-restraints excluded: chain A residue 926 LEU 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 42 MET 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 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 727 SER 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 1026 MET Chi-restraints excluded: chain B residue 1036 THR 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 142 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN A 952 GLN ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN 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 = 0.3708 r_free = 0.3708 target = 0.144853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118040 restraints weight = 24080.096| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.80 r_work: 0.3287 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20778 Z= 0.168 Angle : 0.568 13.326 28141 Z= 0.298 Chirality : 0.045 0.263 3141 Planarity : 0.004 0.091 3624 Dihedral : 5.104 34.802 2737 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 2.06 % Allowed : 21.01 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.17), residues: 2526 helix: 0.89 (0.21), residues: 641 sheet: -1.53 (0.22), residues: 501 loop : -1.15 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 901 TYR 0.023 0.002 TYR B 12 PHE 0.019 0.001 PHE B 438 TRP 0.014 0.001 TRP A 629 HIS 0.004 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00403 (20777) covalent geometry : angle 0.56766 (28139) SS BOND : bond 0.00214 ( 1) SS BOND : angle 1.77505 ( 2) hydrogen bonds : bond 0.03316 ( 694) hydrogen bonds : angle 4.83894 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6751.18 seconds wall clock time: 116 minutes 14.80 seconds (6974.80 seconds total)