Starting phenix.real_space_refine on Thu Sep 18 04:19:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jb6_6408/09_2025/3jb6_6408.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jb6_6408/09_2025/3jb6_6408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jb6_6408/09_2025/3jb6_6408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jb6_6408/09_2025/3jb6_6408.map" model { file = "/net/cci-nas-00/data/ceres_data/3jb6_6408/09_2025/3jb6_6408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jb6_6408/09_2025/3jb6_6408.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 54 5.16 5 C 8821 2.51 5 N 2379 2.21 5 O 2644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13904 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9556 Classifications: {'peptide': 1196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 1154} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3985 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 478} Chain breaks: 2 Chain: "C" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 170 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 129 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.46, per 1000 atoms: 0.25 Number of scatterers: 13904 At special positions: 0 Unit cell: (104.03, 131.3, 110.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 6 15.00 O 2644 8.00 N 2379 7.00 C 8821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.18 Conformation dependent library (CDL) restraints added in 621.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 15 sheets defined 53.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 19 through 34 removed outlier: 3.796A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 removed outlier: 3.573A pdb=" N ARG A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 41 " --> pdb=" O ARG A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.546A pdb=" N ILE A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.541A pdb=" N TYR A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.533A pdb=" N LYS A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 3.661A pdb=" N VAL A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.985A pdb=" N THR A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.588A pdb=" N ILE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.606A pdb=" N GLU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 removed outlier: 3.621A pdb=" N VAL A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 294 through 307 removed outlier: 4.362A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.692A pdb=" N GLN A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.658A pdb=" N THR A 339 " --> pdb=" O CYS A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 388 through 398 removed outlier: 3.746A pdb=" N TYR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.839A pdb=" N LYS A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 424 Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 462 through 472 removed outlier: 4.298A pdb=" N ILE A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 removed outlier: 3.995A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 500' Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.571A pdb=" N GLU A 512 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.935A pdb=" N TRP A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 536 " --> pdb=" O MET A 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 531 through 536' Processing helix chain 'A' and resid 550 through 555 removed outlier: 4.251A pdb=" N SER A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 574 removed outlier: 3.900A pdb=" N ASP A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.808A pdb=" N ALA A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 613 " --> pdb=" O CYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 666 removed outlier: 3.595A pdb=" N HIS A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 652 " --> pdb=" O HIS A 648 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 707 removed outlier: 3.517A pdb=" N TYR A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 739 removed outlier: 3.500A pdb=" N ILE A 739 " --> pdb=" O ALA A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 736 through 739' Processing helix chain 'A' and resid 752 through 767 Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.906A pdb=" N VAL A 771 " --> pdb=" O VAL A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.807A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 removed outlier: 3.602A pdb=" N ASN A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 839 Processing helix chain 'A' and resid 867 through 871 removed outlier: 4.177A pdb=" N TYR A 870 " --> pdb=" O ARG A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 878 removed outlier: 4.016A pdb=" N TYR A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 887 removed outlier: 3.622A pdb=" N GLN A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 900 removed outlier: 3.957A pdb=" N LEU A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 911 Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 932 through 938 Processing helix chain 'A' and resid 942 through 959 removed outlier: 3.531A pdb=" N ARG A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 980 removed outlier: 3.849A pdb=" N LYS A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 980 " --> pdb=" O LYS A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1009 removed outlier: 3.533A pdb=" N ALA A1004 " --> pdb=" O ASP A1000 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1020 Processing helix chain 'A' and resid 1035 through 1040 removed outlier: 4.170A pdb=" N HIS A1039 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A1040 " --> pdb=" O HIS A1036 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1035 through 1040' Processing helix chain 'A' and resid 1053 through 1062 Processing helix chain 'A' and resid 1066 through 1081 removed outlier: 3.510A pdb=" N LEU A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1103 Processing helix chain 'A' and resid 1106 through 1114 Processing helix chain 'A' and resid 1119 through 1135 removed outlier: 3.918A pdb=" N ALA A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1160 removed outlier: 4.524A pdb=" N ARG A1160 " --> pdb=" O SER A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1172 removed outlier: 3.961A pdb=" N VAL A1170 " --> pdb=" O PRO A1166 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER A1171 " --> pdb=" O LYS A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1190 removed outlier: 3.693A pdb=" N ILE A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1193 No H-bonds generated for 'chain 'A' and resid 1191 through 1193' Processing helix chain 'A' and resid 1203 through 1211 Processing helix chain 'A' and resid 1214 through 1219 removed outlier: 3.716A pdb=" N ILE A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.828A pdb=" N TYR B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 63 removed outlier: 3.712A pdb=" N LYS B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS B 63 " --> pdb=" O HIS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 removed outlier: 3.700A pdb=" N TYR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 149 removed outlier: 3.549A pdb=" N LEU B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.835A pdb=" N LEU B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.574A pdb=" N TYR B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 327 through 341 removed outlier: 3.506A pdb=" N GLU B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 338 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.642A pdb=" N PHE B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.773A pdb=" N LYS B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.512A pdb=" N SER B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.586A pdb=" N GLN B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 440 removed outlier: 3.821A pdb=" N LEU B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 461 removed outlier: 3.811A pdb=" N GLU B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 491 through 497 removed outlier: 3.858A pdb=" N ALA B 496 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 520 removed outlier: 3.524A pdb=" N ARG B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 538 Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.685A pdb=" N ILE B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.546A pdb=" N GLN D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 54 through 58 Processing sheet with id=B, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.517A pdb=" N ARG A 191 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 266 through 272 removed outlier: 3.702A pdb=" N GLY A 280 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.734A pdb=" N MET A 373 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN A 383 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL A 371 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 477 through 479 removed outlier: 3.641A pdb=" N VAL A 477 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 487 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 672 through 677 removed outlier: 6.834A pdb=" N ILE A 685 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 675 " --> pdb=" O MET A 683 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET A 683 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE A 677 " --> pdb=" O ASP A 681 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 545 " --> pdb=" O GLU A 714 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'A' and resid 578 through 579 removed outlier: 3.528A pdb=" N PHE A 579 " --> pdb=" O TYR A 582 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'A' and resid 621 through 624 Processing sheet with id=I, first strand: chain 'A' and resid 719 through 721 Processing sheet with id=J, first strand: chain 'A' and resid 813 through 816 removed outlier: 4.370A pdb=" N THR A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 831 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 992 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP A 797 " --> pdb=" O VAL A 994 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 1022 through 1030 removed outlier: 4.826A pdb=" N ARG A1197 " --> pdb=" O GLU A1027 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ARG A1163 " --> pdb=" O MET A1200 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N LEU A1202 " --> pdb=" O ARG A1163 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=M, first strand: chain 'B' and resid 204 through 208 removed outlier: 6.157A pdb=" N ARG B 204 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE B 229 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE B 206 " --> pdb=" O PHE B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=M Processing sheet with id=N, first strand: chain 'B' and resid 297 through 299 removed outlier: 6.663A pdb=" N GLY B 255 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 257 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 316 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR B 259 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'B' and resid 378 through 381 removed outlier: 3.560A pdb=" N GLU B 488 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N VAL B 505 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 350 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 507 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR B 352 " --> pdb=" O LEU B 507 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR B 504 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL B 545 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU B 506 " --> pdb=" O VAL B 545 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1617 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: 2.71 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 87 1.23 - 1.38: 5536 1.38 - 1.53: 8088 1.53 - 1.68: 397 1.68 - 1.83: 95 Bond restraints: 14203 Sorted by residual: bond pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta sigma weight residual 1.466 1.113 0.353 1.50e-02 4.44e+03 5.55e+02 bond pdb=" C ALA C 129 " pdb=" O ALA C 129 " ideal model delta sigma weight residual 1.237 1.077 0.160 1.17e-02 7.31e+03 1.86e+02 bond pdb=" C ASN C 127 " pdb=" O ASN C 127 " ideal model delta sigma weight residual 1.237 1.075 0.161 1.19e-02 7.06e+03 1.84e+02 bond pdb=" C PRO C 132 " pdb=" O PRO C 132 " ideal model delta sigma weight residual 1.233 1.087 0.146 1.13e-02 7.83e+03 1.66e+02 bond pdb=" CA VAL C 120 " pdb=" CB VAL C 120 " ideal model delta sigma weight residual 1.540 1.402 0.138 1.10e-02 8.26e+03 1.58e+02 ... (remaining 14198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 19152 4.12 - 8.25: 84 8.25 - 12.37: 9 12.37 - 16.50: 3 16.50 - 20.62: 2 Bond angle restraints: 19250 Sorted by residual: angle pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" C LEU C 130 " ideal model delta sigma weight residual 113.17 133.79 -20.62 1.26e+00 6.30e-01 2.68e+02 angle pdb=" N ALA C 129 " pdb=" CA ALA C 129 " pdb=" C ALA C 129 " ideal model delta sigma weight residual 111.28 123.26 -11.98 1.09e+00 8.42e-01 1.21e+02 angle pdb=" CA PHE C 121 " pdb=" C PHE C 121 " pdb=" O PHE C 121 " ideal model delta sigma weight residual 120.42 110.93 9.49 1.06e+00 8.90e-01 8.01e+01 angle pdb=" N MET C 133 " pdb=" CA MET C 133 " pdb=" CB MET C 133 " ideal model delta sigma weight residual 110.42 98.63 11.79 1.66e+00 3.63e-01 5.04e+01 angle pdb=" CG1 VAL C 120 " pdb=" CB VAL C 120 " pdb=" CG2 VAL C 120 " ideal model delta sigma weight residual 110.80 95.32 15.48 2.20e+00 2.07e-01 4.95e+01 ... (remaining 19245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.92: 8410 27.92 - 55.84: 88 55.84 - 83.75: 10 83.75 - 111.67: 0 111.67 - 139.59: 2 Dihedral angle restraints: 8510 sinusoidal: 3410 harmonic: 5100 Sorted by residual: dihedral pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual 122.80 145.12 -22.32 0 2.50e+00 1.60e-01 7.97e+01 dihedral pdb=" C LEU C 130 " pdb=" N LEU C 130 " pdb=" CA LEU C 130 " pdb=" CB LEU C 130 " ideal model delta harmonic sigma weight residual -122.60 -144.38 21.78 0 2.50e+00 1.60e-01 7.59e+01 dihedral pdb=" CA SER A 926 " pdb=" C SER A 926 " pdb=" N PRO A 927 " pdb=" CA PRO A 927 " ideal model delta harmonic sigma weight residual 180.00 144.58 35.42 0 5.00e+00 4.00e-02 5.02e+01 ... (remaining 8507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 2136 0.219 - 0.439: 6 0.439 - 0.658: 3 0.658 - 0.878: 1 0.878 - 1.097: 1 Chirality restraints: 2147 Sorted by residual: chirality pdb=" CA LEU C 130 " pdb=" N LEU C 130 " pdb=" C LEU C 130 " pdb=" CB LEU C 130 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" CA PRO D 111 " pdb=" N PRO D 111 " pdb=" C PRO D 111 " pdb=" CB PRO D 111 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA PHE C 121 " pdb=" N PHE C 121 " pdb=" C PHE C 121 " pdb=" CB PHE C 121 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.89e+00 ... (remaining 2144 not shown) Planarity restraints: 2451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 117 " -0.599 9.50e-02 1.11e+02 2.68e-01 4.40e+01 pdb=" NE ARG C 117 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG C 117 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 117 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 117 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " 0.033 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP A 606 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 769 " 0.018 2.00e-02 2.50e+03 2.12e-02 7.87e+00 pdb=" CG PHE A 769 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 769 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 769 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 769 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 769 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 769 " 0.001 2.00e-02 2.50e+03 ... (remaining 2448 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 268 2.68 - 3.23: 13779 3.23 - 3.79: 20379 3.79 - 4.34: 30002 4.34 - 4.90: 48737 Nonbonded interactions: 113165 Sorted by model distance: nonbonded pdb=" OH TYR B 352 " pdb=" OD1 ASP B 495 " model vdw 2.123 3.040 nonbonded pdb=" O CYS A 574 " pdb=" ND2 ASN A 603 " model vdw 2.150 3.120 nonbonded pdb=" O ILE A1190 " pdb=" NH2 ARG D 117 " model vdw 2.175 3.120 nonbonded pdb=" NE2 GLN A 617 " pdb=" OE1 GLU A 634 " model vdw 2.205 3.120 nonbonded pdb=" O CYS A 265 " pdb=" OG1 THR A 286 " model vdw 2.224 3.040 ... (remaining 113160 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 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 : 0.010 0.353 14203 Z= 0.596 Angle : 0.900 20.624 19250 Z= 0.550 Chirality : 0.062 1.097 2147 Planarity : 0.007 0.268 2451 Dihedral : 9.545 139.588 5226 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.45 % Favored : 97.44 % Rotamer: Outliers : 0.20 % Allowed : 1.13 % Favored : 98.67 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 1.79 % 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: -3.72 (0.16), residues: 1717 helix: -3.85 (0.11), residues: 805 sheet: -1.38 (0.35), residues: 143 loop : -0.80 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1175 TYR 0.033 0.002 TYR B 19 PHE 0.049 0.003 PHE A 769 TRP 0.070 0.004 TRP A 606 HIS 0.013 0.002 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.01025 (14203) covalent geometry : angle 0.89999 (19250) hydrogen bonds : bond 0.30985 ( 564) hydrogen bonds : angle 10.45420 ( 1617) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 437 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.9024 (p0) cc_final: 0.8535 (p0) REVERT: A 82 ASP cc_start: 0.9100 (t0) cc_final: 0.8872 (t0) REVERT: A 90 GLU cc_start: 0.8678 (mp0) cc_final: 0.8363 (mp0) REVERT: A 91 ASP cc_start: 0.6927 (t0) cc_final: 0.6503 (p0) REVERT: A 119 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8358 (mtmm) REVERT: A 163 THR cc_start: 0.9278 (m) cc_final: 0.9075 (t) REVERT: A 473 PRO cc_start: 0.8956 (Cg_endo) cc_final: 0.8714 (Cg_exo) REVERT: A 480 GLN cc_start: 0.8466 (mt0) cc_final: 0.8149 (mt0) REVERT: A 596 GLN cc_start: 0.9053 (mt0) cc_final: 0.8665 (mp10) REVERT: A 623 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7370 (tt0) REVERT: A 703 ILE cc_start: 0.9024 (tt) cc_final: 0.8701 (tt) REVERT: A 809 SER cc_start: 0.8908 (t) cc_final: 0.8632 (p) REVERT: A 884 MET cc_start: 0.9155 (mtp) cc_final: 0.8920 (mtm) REVERT: A 889 SER cc_start: 0.8683 (m) cc_final: 0.8312 (p) REVERT: A 950 ARG cc_start: 0.8493 (ttt-90) cc_final: 0.8164 (ttp80) REVERT: A 961 HIS cc_start: 0.8440 (m90) cc_final: 0.8185 (m90) REVERT: A 967 ILE cc_start: 0.8318 (mt) cc_final: 0.8116 (mt) REVERT: A 1010 LYS cc_start: 0.8627 (ptpt) cc_final: 0.8218 (pttt) REVERT: A 1138 GLU cc_start: 0.8523 (pm20) cc_final: 0.8150 (pt0) REVERT: B 136 LYS cc_start: 0.8569 (tttt) cc_final: 0.7969 (tmtt) REVERT: B 149 ARG cc_start: 0.8773 (mtt90) cc_final: 0.8537 (mtt-85) REVERT: B 235 GLU cc_start: 0.8678 (tt0) cc_final: 0.8326 (mp0) REVERT: B 277 ASP cc_start: 0.8686 (m-30) cc_final: 0.8376 (m-30) REVERT: B 395 ASP cc_start: 0.8587 (m-30) cc_final: 0.8331 (m-30) REVERT: B 431 ILE cc_start: 0.9106 (mm) cc_final: 0.8842 (mm) REVERT: B 443 ARG cc_start: 0.8957 (mtp85) cc_final: 0.8753 (mtp-110) REVERT: B 553 SER cc_start: 0.9563 (t) cc_final: 0.9349 (p) REVERT: B 558 LYS cc_start: 0.8815 (pttt) cc_final: 0.8384 (tttm) outliers start: 3 outliers final: 2 residues processed: 440 average time/residue: 0.1649 time to fit residues: 98.5871 Evaluate side-chains 286 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 130 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 413 HIS A 525 ASN A 725 GLN A 898 HIS A1020 HIS A1070 ASN A1108 ASN A1147 GLN B 212 ASN B 231 ASN B 369 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.112229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.093091 restraints weight = 18051.480| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.75 r_work: 0.2691 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14203 Z= 0.266 Angle : 0.678 8.738 19250 Z= 0.355 Chirality : 0.047 0.158 2147 Planarity : 0.005 0.062 2451 Dihedral : 7.775 136.979 1948 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.46 % Allowed : 7.64 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 1.79 % 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: -2.12 (0.17), residues: 1717 helix: -1.89 (0.15), residues: 824 sheet: -1.17 (0.36), residues: 134 loop : -0.63 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 168 TYR 0.026 0.002 TYR A 242 PHE 0.023 0.002 PHE A 902 TRP 0.047 0.003 TRP A 606 HIS 0.010 0.002 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00645 (14203) covalent geometry : angle 0.67797 (19250) hydrogen bonds : bond 0.05431 ( 564) hydrogen bonds : angle 5.51479 ( 1617) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 298 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8319 (mttt) cc_final: 0.7988 (mtpt) REVERT: A 28 HIS cc_start: 0.8325 (t70) cc_final: 0.8115 (t70) REVERT: A 37 ARG cc_start: 0.8702 (ttp80) cc_final: 0.8494 (ttp80) REVERT: A 90 GLU cc_start: 0.8219 (mp0) cc_final: 0.7857 (mp0) REVERT: A 91 ASP cc_start: 0.6742 (t0) cc_final: 0.6255 (p0) REVERT: A 373 MET cc_start: 0.9336 (ttm) cc_final: 0.9134 (ttm) REVERT: A 375 ASN cc_start: 0.8434 (t0) cc_final: 0.8232 (t0) REVERT: A 479 ARG cc_start: 0.8159 (ttp-170) cc_final: 0.7769 (mtp180) REVERT: A 596 GLN cc_start: 0.8778 (mt0) cc_final: 0.8513 (mp10) REVERT: A 623 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7501 (tt0) REVERT: A 703 ILE cc_start: 0.8854 (tt) cc_final: 0.8513 (tt) REVERT: A 809 SER cc_start: 0.8958 (t) cc_final: 0.8541 (p) REVERT: A 947 GLU cc_start: 0.8500 (tp30) cc_final: 0.8128 (tp30) REVERT: A 961 HIS cc_start: 0.8262 (m90) cc_final: 0.8002 (m90) REVERT: A 966 ASP cc_start: 0.8286 (p0) cc_final: 0.7992 (p0) REVERT: A 996 SER cc_start: 0.8337 (m) cc_final: 0.8121 (p) REVERT: A 1010 LYS cc_start: 0.8544 (ptpt) cc_final: 0.8247 (pttp) REVERT: A 1138 GLU cc_start: 0.8564 (pm20) cc_final: 0.8045 (pt0) REVERT: B 160 ASP cc_start: 0.8606 (t0) cc_final: 0.8351 (t0) REVERT: B 241 LYS cc_start: 0.8601 (tptt) cc_final: 0.8213 (tptt) REVERT: B 277 ASP cc_start: 0.8483 (m-30) cc_final: 0.8220 (m-30) REVERT: B 558 LYS cc_start: 0.8570 (pttt) cc_final: 0.8330 (tttm) outliers start: 22 outliers final: 15 residues processed: 312 average time/residue: 0.1424 time to fit residues: 63.0212 Evaluate side-chains 280 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 265 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 123 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 84 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 64 GLN A 236 HIS A 525 ASN A 725 GLN A 807 ASN A1108 ASN B 170 ASN B 369 GLN B 393 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.110338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.092810 restraints weight = 18223.690| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.52 r_work: 0.2770 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14203 Z= 0.142 Angle : 0.534 7.473 19250 Z= 0.278 Chirality : 0.041 0.149 2147 Planarity : 0.004 0.063 2451 Dihedral : 7.320 137.658 1946 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.53 % Allowed : 9.23 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.19), residues: 1717 helix: -0.53 (0.17), residues: 831 sheet: -0.69 (0.39), residues: 139 loop : -0.40 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 252 TYR 0.017 0.001 TYR A 242 PHE 0.016 0.001 PHE A 902 TRP 0.028 0.001 TRP A 606 HIS 0.004 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00337 (14203) covalent geometry : angle 0.53391 (19250) hydrogen bonds : bond 0.03919 ( 564) hydrogen bonds : angle 4.81403 ( 1617) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8425 (mttt) cc_final: 0.8157 (mtpt) REVERT: A 37 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8368 (ttp80) REVERT: A 165 TYR cc_start: 0.9293 (p90) cc_final: 0.9072 (p90) REVERT: A 479 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7779 (mtp180) REVERT: A 561 ASP cc_start: 0.8827 (t0) cc_final: 0.8521 (t0) REVERT: A 612 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8256 (tm-30) REVERT: A 807 ASN cc_start: 0.7880 (m110) cc_final: 0.7655 (m-40) REVERT: A 809 SER cc_start: 0.8927 (t) cc_final: 0.8527 (p) REVERT: A 961 HIS cc_start: 0.8357 (m90) cc_final: 0.8150 (m90) REVERT: A 966 ASP cc_start: 0.8212 (p0) cc_final: 0.7949 (p0) REVERT: A 1049 MET cc_start: 0.9294 (ptm) cc_final: 0.9033 (ptp) REVERT: A 1082 ASN cc_start: 0.8372 (t0) cc_final: 0.7621 (p0) REVERT: A 1089 ASP cc_start: 0.8648 (m-30) cc_final: 0.8403 (m-30) REVERT: A 1138 GLU cc_start: 0.8712 (pm20) cc_final: 0.8041 (pt0) REVERT: B 160 ASP cc_start: 0.8618 (t0) cc_final: 0.8142 (t0) REVERT: B 277 ASP cc_start: 0.8373 (m-30) cc_final: 0.8144 (m-30) REVERT: B 510 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.8964 (pp) outliers start: 23 outliers final: 15 residues processed: 307 average time/residue: 0.1432 time to fit residues: 62.1452 Evaluate side-chains 278 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 262 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain D residue 123 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 128 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 276 ASN A 525 ASN A 617 GLN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN B 63 HIS B 231 ASN B 369 GLN C 131 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.106689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.089123 restraints weight = 18303.452| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.54 r_work: 0.2752 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14203 Z= 0.260 Angle : 0.614 8.201 19250 Z= 0.319 Chirality : 0.045 0.155 2147 Planarity : 0.004 0.061 2451 Dihedral : 7.516 142.365 1946 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.92 % Allowed : 9.50 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 1717 helix: -0.30 (0.18), residues: 824 sheet: -0.74 (0.41), residues: 138 loop : -0.43 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1073 TYR 0.023 0.002 TYR A 242 PHE 0.021 0.002 PHE A 902 TRP 0.031 0.002 TRP A 606 HIS 0.011 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00633 (14203) covalent geometry : angle 0.61428 (19250) hydrogen bonds : bond 0.04584 ( 564) hydrogen bonds : angle 4.84610 ( 1617) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8470 (mttt) cc_final: 0.8120 (mtpt) REVERT: A 37 ARG cc_start: 0.8945 (ttp80) cc_final: 0.8733 (ttp80) REVERT: A 373 MET cc_start: 0.9328 (ttm) cc_final: 0.9053 (ttm) REVERT: A 473 PRO cc_start: 0.8605 (Cg_endo) cc_final: 0.8347 (Cg_exo) REVERT: A 479 ARG cc_start: 0.8191 (ttp-170) cc_final: 0.7754 (mtp180) REVERT: A 561 ASP cc_start: 0.8834 (t0) cc_final: 0.8512 (t0) REVERT: A 706 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7933 (mm-30) REVERT: A 766 ASP cc_start: 0.9135 (t0) cc_final: 0.8909 (t0) REVERT: A 809 SER cc_start: 0.8994 (t) cc_final: 0.8550 (p) REVERT: A 961 HIS cc_start: 0.8341 (m90) cc_final: 0.8082 (m90) REVERT: A 1049 MET cc_start: 0.9322 (ptm) cc_final: 0.9091 (ptp) REVERT: A 1082 ASN cc_start: 0.8397 (t0) cc_final: 0.7633 (p0) REVERT: A 1138 GLU cc_start: 0.8780 (pm20) cc_final: 0.7994 (pt0) REVERT: B 141 MET cc_start: 0.9176 (tpt) cc_final: 0.8720 (tpt) REVERT: B 160 ASP cc_start: 0.8645 (t0) cc_final: 0.8174 (t0) REVERT: B 161 ASP cc_start: 0.8742 (t0) cc_final: 0.8494 (t0) REVERT: B 510 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9127 (pt) outliers start: 44 outliers final: 31 residues processed: 292 average time/residue: 0.1396 time to fit residues: 57.8138 Evaluate side-chains 285 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain D residue 123 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 121 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 169 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 63 HIS B 369 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.110551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.093518 restraints weight = 18078.096| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.46 r_work: 0.2771 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14203 Z= 0.109 Angle : 0.496 8.292 19250 Z= 0.256 Chirality : 0.040 0.140 2147 Planarity : 0.003 0.054 2451 Dihedral : 7.128 141.344 1946 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 11.22 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1717 helix: 0.40 (0.18), residues: 822 sheet: -0.35 (0.42), residues: 141 loop : -0.20 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 252 TYR 0.015 0.001 TYR A 805 PHE 0.010 0.001 PHE A 902 TRP 0.017 0.001 TRP A 606 HIS 0.005 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00252 (14203) covalent geometry : angle 0.49603 (19250) hydrogen bonds : bond 0.03221 ( 564) hydrogen bonds : angle 4.44639 ( 1617) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8426 (mttt) cc_final: 0.8122 (mtpt) REVERT: A 90 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7931 (mp0) REVERT: A 133 MET cc_start: 0.9126 (ttp) cc_final: 0.8909 (ttp) REVERT: A 165 TYR cc_start: 0.9277 (p90) cc_final: 0.9072 (p90) REVERT: A 473 PRO cc_start: 0.8527 (Cg_endo) cc_final: 0.8275 (Cg_exo) REVERT: A 479 ARG cc_start: 0.8082 (ttp-170) cc_final: 0.7664 (mtp180) REVERT: A 561 ASP cc_start: 0.8815 (t0) cc_final: 0.8402 (t0) REVERT: A 706 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 809 SER cc_start: 0.8991 (t) cc_final: 0.8591 (p) REVERT: A 1082 ASN cc_start: 0.8301 (t0) cc_final: 0.7613 (p0) REVERT: A 1138 GLU cc_start: 0.8756 (pm20) cc_final: 0.7918 (pt0) REVERT: B 141 MET cc_start: 0.9141 (tpt) cc_final: 0.8652 (tpt) REVERT: B 160 ASP cc_start: 0.8630 (t0) cc_final: 0.8108 (t0) REVERT: B 364 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8821 (m) REVERT: B 510 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8968 (pp) outliers start: 30 outliers final: 22 residues processed: 310 average time/residue: 0.1377 time to fit residues: 60.0680 Evaluate side-chains 295 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 271 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain D residue 123 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 39 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 525 ASN B 63 HIS B 170 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.113638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.096595 restraints weight = 17800.917| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.47 r_work: 0.2801 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14203 Z= 0.085 Angle : 0.472 8.064 19250 Z= 0.244 Chirality : 0.039 0.137 2147 Planarity : 0.003 0.052 2451 Dihedral : 6.802 140.262 1946 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.86 % Allowed : 12.08 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.20), residues: 1717 helix: 0.84 (0.19), residues: 828 sheet: -0.24 (0.42), residues: 151 loop : -0.13 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 252 TYR 0.014 0.001 TYR A 805 PHE 0.007 0.001 PHE B 335 TRP 0.011 0.001 TRP B 260 HIS 0.004 0.000 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00184 (14203) covalent geometry : angle 0.47236 (19250) hydrogen bonds : bond 0.02752 ( 564) hydrogen bonds : angle 4.21727 ( 1617) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 307 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8252 (ttp80) REVERT: A 90 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7896 (mp0) REVERT: A 277 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8571 (tt0) REVERT: A 360 ARG cc_start: 0.8511 (ptt180) cc_final: 0.8192 (ptt90) REVERT: A 374 SER cc_start: 0.9342 (p) cc_final: 0.8981 (m) REVERT: A 479 ARG cc_start: 0.8033 (ttp-170) cc_final: 0.7598 (mtp180) REVERT: A 561 ASP cc_start: 0.8776 (t0) cc_final: 0.8305 (t0) REVERT: A 706 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 809 SER cc_start: 0.8903 (t) cc_final: 0.8461 (p) REVERT: A 844 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: A 966 ASP cc_start: 0.8174 (p0) cc_final: 0.7788 (p0) REVERT: A 1082 ASN cc_start: 0.8325 (t0) cc_final: 0.7596 (p0) REVERT: A 1138 GLU cc_start: 0.8752 (pm20) cc_final: 0.7906 (pt0) REVERT: B 160 ASP cc_start: 0.8584 (t0) cc_final: 0.8024 (t0) REVERT: B 510 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8946 (pp) outliers start: 28 outliers final: 15 residues processed: 325 average time/residue: 0.1418 time to fit residues: 65.3024 Evaluate side-chains 292 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain D residue 123 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 145 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.108437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.091018 restraints weight = 18112.186| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.48 r_work: 0.2735 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14203 Z= 0.187 Angle : 0.550 10.274 19250 Z= 0.282 Chirality : 0.042 0.143 2147 Planarity : 0.004 0.050 2451 Dihedral : 6.914 141.793 1943 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.86 % Allowed : 11.89 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.20), residues: 1717 helix: 0.63 (0.18), residues: 835 sheet: -0.21 (0.44), residues: 136 loop : -0.21 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 252 TYR 0.018 0.001 TYR A 805 PHE 0.014 0.002 PHE B 335 TRP 0.024 0.002 TRP A 606 HIS 0.006 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00455 (14203) covalent geometry : angle 0.54979 (19250) hydrogen bonds : bond 0.03792 ( 564) hydrogen bonds : angle 4.43383 ( 1617) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 TYR cc_start: 0.9291 (p90) cc_final: 0.9029 (p90) REVERT: A 360 ARG cc_start: 0.8693 (ptt180) cc_final: 0.8355 (ptt90) REVERT: A 479 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7581 (mtp180) REVERT: A 561 ASP cc_start: 0.8865 (t0) cc_final: 0.8464 (t0) REVERT: A 706 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 809 SER cc_start: 0.8931 (t) cc_final: 0.8508 (p) REVERT: A 966 ASP cc_start: 0.8080 (p0) cc_final: 0.7671 (p0) REVERT: A 1049 MET cc_start: 0.9404 (ptm) cc_final: 0.9156 (ptp) REVERT: A 1082 ASN cc_start: 0.8369 (t0) cc_final: 0.7630 (p0) REVERT: A 1138 GLU cc_start: 0.8788 (pm20) cc_final: 0.7921 (pt0) REVERT: A 1192 ASN cc_start: 0.8924 (t0) cc_final: 0.8720 (t0) REVERT: B 160 ASP cc_start: 0.8622 (t0) cc_final: 0.8130 (t0) REVERT: B 510 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9061 (pt) REVERT: C 133 MET cc_start: 0.6524 (OUTLIER) cc_final: 0.4922 (tpp) outliers start: 43 outliers final: 35 residues processed: 292 average time/residue: 0.1421 time to fit residues: 58.6983 Evaluate side-chains 295 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 258 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain A residue 1190 ILE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain D residue 123 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 63 HIS B 369 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.109810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.092279 restraints weight = 17890.177| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.51 r_work: 0.2763 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14203 Z= 0.125 Angle : 0.514 10.130 19250 Z= 0.262 Chirality : 0.040 0.141 2147 Planarity : 0.004 0.048 2451 Dihedral : 6.803 140.760 1943 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.26 % Allowed : 13.15 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.20), residues: 1717 helix: 0.78 (0.18), residues: 836 sheet: -0.36 (0.41), residues: 151 loop : -0.20 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 252 TYR 0.017 0.001 TYR A 805 PHE 0.012 0.001 PHE A 902 TRP 0.017 0.001 TRP A 606 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00297 (14203) covalent geometry : angle 0.51389 (19250) hydrogen bonds : bond 0.03250 ( 564) hydrogen bonds : angle 4.31708 ( 1617) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 TYR cc_start: 0.9255 (p90) cc_final: 0.8859 (p90) REVERT: A 360 ARG cc_start: 0.8668 (ptt180) cc_final: 0.8326 (ptt90) REVERT: A 479 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7610 (mtp180) REVERT: A 561 ASP cc_start: 0.8830 (t0) cc_final: 0.8411 (t0) REVERT: A 706 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 809 SER cc_start: 0.8979 (t) cc_final: 0.8589 (p) REVERT: A 844 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6885 (mt-10) REVERT: A 966 ASP cc_start: 0.8091 (p0) cc_final: 0.7882 (p0) REVERT: A 1049 MET cc_start: 0.9358 (ptm) cc_final: 0.9005 (ptp) REVERT: A 1082 ASN cc_start: 0.8387 (t0) cc_final: 0.7651 (p0) REVERT: A 1138 GLU cc_start: 0.8813 (pm20) cc_final: 0.7895 (pt0) REVERT: A 1192 ASN cc_start: 0.8891 (t0) cc_final: 0.8639 (t0) REVERT: B 160 ASP cc_start: 0.8618 (t0) cc_final: 0.8101 (t0) REVERT: B 510 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9021 (pt) outliers start: 34 outliers final: 26 residues processed: 296 average time/residue: 0.1346 time to fit residues: 56.5539 Evaluate side-chains 291 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain D residue 123 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 146 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 63 HIS B 369 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.107531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.090167 restraints weight = 18129.311| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.47 r_work: 0.2693 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14203 Z= 0.203 Angle : 0.575 11.973 19250 Z= 0.295 Chirality : 0.043 0.148 2147 Planarity : 0.004 0.052 2451 Dihedral : 7.005 141.819 1943 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.52 % Allowed : 12.95 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.20), residues: 1717 helix: 0.54 (0.18), residues: 843 sheet: -0.45 (0.43), residues: 134 loop : -0.30 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.019 0.002 TYR A 805 PHE 0.016 0.002 PHE A 902 TRP 0.024 0.002 TRP A 606 HIS 0.005 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00494 (14203) covalent geometry : angle 0.57482 (19250) hydrogen bonds : bond 0.03915 ( 564) hydrogen bonds : angle 4.48719 ( 1617) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8470 (mttt) cc_final: 0.8146 (mtpt) REVERT: A 165 TYR cc_start: 0.9307 (p90) cc_final: 0.9063 (p90) REVERT: A 360 ARG cc_start: 0.8681 (ptt180) cc_final: 0.8334 (ptt90) REVERT: A 479 ARG cc_start: 0.8039 (ttp-170) cc_final: 0.7548 (mtp180) REVERT: A 561 ASP cc_start: 0.8865 (t0) cc_final: 0.8476 (t0) REVERT: A 706 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 766 ASP cc_start: 0.9151 (t0) cc_final: 0.8897 (t0) REVERT: A 809 SER cc_start: 0.8967 (t) cc_final: 0.8498 (p) REVERT: A 895 ASP cc_start: 0.8191 (t0) cc_final: 0.7977 (t0) REVERT: A 966 ASP cc_start: 0.8163 (p0) cc_final: 0.7762 (p0) REVERT: A 1049 MET cc_start: 0.9389 (ptm) cc_final: 0.9142 (ptp) REVERT: A 1082 ASN cc_start: 0.8411 (t0) cc_final: 0.7651 (p0) REVERT: A 1138 GLU cc_start: 0.8810 (pm20) cc_final: 0.7903 (pt0) REVERT: A 1192 ASN cc_start: 0.8925 (t0) cc_final: 0.8607 (t0) REVERT: B 160 ASP cc_start: 0.8630 (t0) cc_final: 0.8144 (t0) REVERT: B 354 GLU cc_start: 0.8313 (tt0) cc_final: 0.8089 (tt0) REVERT: B 510 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9058 (pt) REVERT: C 133 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.4920 (tpp) outliers start: 38 outliers final: 32 residues processed: 285 average time/residue: 0.1466 time to fit residues: 59.2659 Evaluate side-chains 294 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 133 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 121 optimal weight: 0.0370 chunk 154 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 63 HIS B 369 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.111563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.093901 restraints weight = 17921.395| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.53 r_work: 0.2804 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14203 Z= 0.112 Angle : 0.511 12.796 19250 Z= 0.261 Chirality : 0.040 0.138 2147 Planarity : 0.003 0.046 2451 Dihedral : 6.783 139.676 1943 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.26 % Allowed : 13.61 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1717 helix: 0.78 (0.18), residues: 847 sheet: -0.50 (0.41), residues: 149 loop : -0.23 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 951 TYR 0.017 0.001 TYR A 805 PHE 0.010 0.001 PHE B 335 TRP 0.014 0.001 TRP A 606 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00261 (14203) covalent geometry : angle 0.51061 (19250) hydrogen bonds : bond 0.03119 ( 564) hydrogen bonds : angle 4.31435 ( 1617) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3434 Ramachandran restraints generated. 1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 165 TYR cc_start: 0.9261 (p90) cc_final: 0.8836 (p90) REVERT: A 360 ARG cc_start: 0.8619 (ptt180) cc_final: 0.8276 (ptt90) REVERT: A 479 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7589 (mtp180) REVERT: A 480 GLN cc_start: 0.8626 (mt0) cc_final: 0.8402 (mt0) REVERT: A 561 ASP cc_start: 0.8800 (t0) cc_final: 0.8387 (t0) REVERT: A 706 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 809 SER cc_start: 0.8921 (t) cc_final: 0.8492 (p) REVERT: A 884 MET cc_start: 0.9209 (mtt) cc_final: 0.8979 (mtt) REVERT: A 895 ASP cc_start: 0.8106 (t0) cc_final: 0.7893 (t0) REVERT: A 912 ASN cc_start: 0.8905 (t0) cc_final: 0.8394 (t0) REVERT: A 966 ASP cc_start: 0.8243 (p0) cc_final: 0.7781 (p0) REVERT: A 1049 MET cc_start: 0.9338 (ptm) cc_final: 0.9016 (ptp) REVERT: A 1082 ASN cc_start: 0.8375 (t0) cc_final: 0.7662 (p0) REVERT: A 1138 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7850 (pt0) REVERT: A 1192 ASN cc_start: 0.8860 (t0) cc_final: 0.8576 (t0) REVERT: B 160 ASP cc_start: 0.8649 (t0) cc_final: 0.8130 (t0) REVERT: B 354 GLU cc_start: 0.8295 (tt0) cc_final: 0.8073 (tt0) REVERT: B 510 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9010 (pt) REVERT: C 133 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.4898 (tpp) outliers start: 34 outliers final: 28 residues processed: 292 average time/residue: 0.1379 time to fit residues: 57.1284 Evaluate side-chains 300 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 269 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 681 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 889 SER Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1153 ASP Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 133 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 94 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 115 optimal weight: 0.0070 chunk 32 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 overall best weight: 2.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A1095 GLN B 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.110806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.093124 restraints weight = 17817.996| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.52 r_work: 0.2805 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14203 Z= 0.133 Angle : 0.523 13.532 19250 Z= 0.268 Chirality : 0.041 0.139 2147 Planarity : 0.004 0.046 2451 Dihedral : 6.761 139.249 1943 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.26 % Allowed : 13.55 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.20), residues: 1717 helix: 0.79 (0.18), residues: 844 sheet: -0.51 (0.40), residues: 149 loop : -0.20 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 149 TYR 0.018 0.001 TYR A 805 PHE 0.011 0.001 PHE B 335 TRP 0.019 0.001 TRP A 606 HIS 0.004 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00318 (14203) covalent geometry : angle 0.52334 (19250) hydrogen bonds : bond 0.03281 ( 564) hydrogen bonds : angle 4.33888 ( 1617) =============================================================================== Job complete usr+sys time: 3339.62 seconds wall clock time: 58 minutes 10.50 seconds (3490.50 seconds total)