Starting phenix.real_space_refine on Sun Sep 13 13:06:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mr3_23955/09_2026/7mr3_23955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mr3_23955/09_2026/7mr3_23955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mr3_23955/09_2026/7mr3_23955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mr3_23955/09_2026/7mr3_23955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mr3_23955/09_2026/7mr3_23955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mr3_23955/09_2026/7mr3_23955.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 40 5.49 5 S 101 5.16 5 C 14801 2.51 5 N 4181 2.21 5 O 4492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23615 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 9043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1128, 9043 Classifications: {'peptide': 1128} Link IDs: {'PTRANS': 50, 'TRANS': 1077} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4672 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 25, 'TRANS': 579} Chain: "X" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 492 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 4.85, per 1000 atoms: 0.21 Number of scatterers: 23615 At special positions: 0 Unit cell: (129.8, 119.9, 146.3, 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 101 16.00 P 40 15.00 O 4492 8.00 N 4181 7.00 C 14801 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5386 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 17 sheets defined 55.7% alpha, 8.4% beta 10 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.806A pdb=" N ALA B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.763A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 156 through 172 removed outlier: 3.543A pdb=" N CYS B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.678A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 5.744A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.620A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.843A pdb=" N ARG B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.683A pdb=" N SER B 279 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 281 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.866A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.270A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.363A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.691A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.938A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.616A pdb=" N ASN B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 removed outlier: 3.525A pdb=" N GLN B 485 " --> pdb=" O GLY B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 510 through 534 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 560 through 574 removed outlier: 4.197A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 4.217A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.837A pdb=" N ALA B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 632 Processing helix chain 'B' and resid 634 through 656 Processing helix chain 'B' and resid 657 through 669 Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.858A pdb=" N LEU B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.086A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.629A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.565A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 removed outlier: 3.611A pdb=" N GLN B 835 " --> pdb=" O ASP B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 843 Processing helix chain 'B' and resid 849 through 860 removed outlier: 4.048A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 949 through 959 Processing helix chain 'B' and resid 969 through 980 Processing helix chain 'B' and resid 983 through 985 No H-bonds generated for 'chain 'B' and resid 983 through 985' Processing helix chain 'B' and resid 986 through 999 removed outlier: 3.625A pdb=" N GLN B 999 " --> pdb=" O THR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'B' and resid 1013 through 1017 removed outlier: 3.861A pdb=" N LYS B1017 " --> pdb=" O ALA B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.652A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1093 removed outlier: 3.628A pdb=" N ALA B1092 " --> pdb=" O ASP B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1105 removed outlier: 3.744A pdb=" N MET B1098 " --> pdb=" O THR B1094 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B1099 " --> pdb=" O GLN B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1126 Processing helix chain 'B' and resid 1130 through 1135 Processing helix chain 'B' and resid 1163 through 1173 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.634A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.566A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 4.065A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.206A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.621A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 262 removed outlier: 3.759A pdb=" N THR C 262 " --> pdb=" O LYS C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 262' Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.713A pdb=" N GLU C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.646A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 removed outlier: 4.101A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.522A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 417 removed outlier: 3.670A pdb=" N SER C 417 " --> pdb=" O ASP C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 430 through 434 removed outlier: 3.835A pdb=" N TYR C 434 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.873A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 513 removed outlier: 3.633A pdb=" N VAL C 511 " --> pdb=" O ASP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 605 through 626 Processing helix chain 'C' and resid 633 through 645 removed outlier: 3.955A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 795 removed outlier: 4.102A pdb=" N TYR C 794 " --> pdb=" O ASP C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 805 No H-bonds generated for 'chain 'C' and resid 803 through 805' Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.185A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 852 Processing helix chain 'C' and resid 874 through 890 removed outlier: 4.037A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 904 removed outlier: 4.611A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 933 removed outlier: 3.762A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 Processing helix chain 'C' and resid 1000 through 1004 removed outlier: 3.854A pdb=" N ASP C1003 " --> pdb=" O LEU C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1031 Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'C' and resid 1060 through 1076 Processing helix chain 'C' and resid 1087 through 1092 Processing helix chain 'C' and resid 1098 through 1120 removed outlier: 3.761A pdb=" N LEU C1114 " --> pdb=" O GLN C1110 " (cutoff:3.500A) Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.694A pdb=" N THR D 36 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 59 removed outlier: 3.713A pdb=" N LEU D 58 " --> pdb=" O PRO D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 80 through 87 Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 223 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.509A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 365 through 375 removed outlier: 4.006A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.911A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 removed outlier: 4.041A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP D 392 " --> pdb=" O ASP D 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 392' Processing helix chain 'D' and resid 400 through 424 removed outlier: 3.909A pdb=" N ALA D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.519A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.514A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 542 removed outlier: 4.041A pdb=" N GLN D 542 " --> pdb=" O HIS D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 539 through 542' Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 Processing helix chain 'D' and resid 599 through 606 removed outlier: 3.529A pdb=" N SER D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.281A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TYR B 441 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 20 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU B 60 " --> pdb=" O MET B 382 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.302A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.673A pdb=" N TYR B 768 " --> pdb=" O VAL B 777 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.307A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N SER B 814 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 752 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLY B 816 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 754 " --> pdb=" O GLY B 816 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS B 500 " --> pdb=" O LEU B 815 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL B 817 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TRP B 502 " --> pdb=" O VAL B 817 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1019 through 1024 removed outlier: 6.722A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B1068 " --> pdb=" O LEU B1079 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B1156 " --> pdb=" O TYR B1140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.691A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ALA C 325 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N HIS C 6 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C 324 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 264 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 272 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.319A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439 removed outlier: 7.184A pdb=" N LYS C 673 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.971A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 650 " --> pdb=" O ARG C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 831 through 833 removed outlier: 5.067A pdb=" N GLN C 951 " --> pdb=" O CYS C 947 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS C 947 " --> pdb=" O GLN C 951 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR C 953 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU C 945 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TRP C 955 " --> pdb=" O ILE C 943 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 943 " --> pdb=" O TRP C 955 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET C 941 " --> pdb=" O PRO C 957 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 831 through 833 removed outlier: 15.771A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.357A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AB5, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.586A pdb=" N SER D 238 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 535 through 537 removed outlier: 8.800A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N PHE D 546 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG D 576 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS D 548 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 535 through 537 removed outlier: 8.800A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR D 580 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU D 551 " --> pdb=" O TYR D 580 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 481 through 483 removed outlier: 6.548A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 509 " --> pdb=" O LEU D 502 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3971 1.32 - 1.44: 6595 1.44 - 1.57: 13402 1.57 - 1.70: 78 1.70 - 1.82: 169 Bond restraints: 24215 Sorted by residual: bond pdb=" C3' DA X 12 " pdb=" O3' DA X 12 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.12e+01 bond pdb=" C3' DG A 63 " pdb=" C2' DG A 63 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DA A 57 " pdb=" C2' DA A 57 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.85e+00 bond pdb=" C3' DT X 15 " pdb=" C2' DT X 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.34e+00 bond pdb=" C3' DT X 22 " pdb=" C2' DT X 22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.04e+00 ... (remaining 24210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 32579 2.96 - 5.91: 385 5.91 - 8.87: 50 8.87 - 11.83: 12 11.83 - 14.79: 2 Bond angle restraints: 33028 Sorted by residual: angle pdb=" N GLN B1112 " pdb=" CA GLN B1112 " pdb=" CB GLN B1112 " ideal model delta sigma weight residual 110.16 117.99 -7.83 1.48e+00 4.57e-01 2.80e+01 angle pdb=" CA GLN B1112 " pdb=" CB GLN B1112 " pdb=" CG GLN B1112 " ideal model delta sigma weight residual 114.10 123.96 -9.86 2.00e+00 2.50e-01 2.43e+01 angle pdb=" CB MET B 136 " pdb=" CG MET B 136 " pdb=" SD MET B 136 " ideal model delta sigma weight residual 112.70 126.43 -13.73 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N ILE B 179 " pdb=" CA ILE B 179 " pdb=" C ILE B 179 " ideal model delta sigma weight residual 112.96 108.66 4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" CA LEU C 655 " pdb=" CB LEU C 655 " pdb=" CG LEU C 655 " ideal model delta sigma weight residual 116.30 131.09 -14.79 3.50e+00 8.16e-02 1.78e+01 ... (remaining 33023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 12637 18.01 - 36.01: 1469 36.01 - 54.02: 321 54.02 - 72.03: 82 72.03 - 90.03: 29 Dihedral angle restraints: 14538 sinusoidal: 6228 harmonic: 8310 Sorted by residual: dihedral pdb=" CA GLU B1029 " pdb=" C GLU B1029 " pdb=" N PRO B1030 " pdb=" CA PRO B1030 " ideal model delta harmonic sigma weight residual 180.00 -148.18 -31.82 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA GLY B1137 " pdb=" C GLY B1137 " pdb=" N VAL B1138 " pdb=" CA VAL B1138 " ideal model delta harmonic sigma weight residual -180.00 -150.03 -29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA TRP B 878 " pdb=" C TRP B 878 " pdb=" N GLN B 879 " pdb=" CA GLN B 879 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 14535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2527 0.047 - 0.094: 815 0.094 - 0.141: 247 0.141 - 0.188: 31 0.188 - 0.235: 7 Chirality restraints: 3627 Sorted by residual: chirality pdb=" CA GLN B1112 " pdb=" N GLN B1112 " pdb=" C GLN B1112 " pdb=" CB GLN B1112 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR B 304 " pdb=" CA THR B 304 " pdb=" OG1 THR B 304 " pdb=" CG2 THR B 304 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP C 484 " pdb=" N ASP C 484 " pdb=" C ASP C 484 " pdb=" CB ASP C 484 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3624 not shown) Planarity restraints: 4202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 878 " 0.026 2.00e-02 2.50e+03 1.88e-02 8.84e+00 pdb=" CG TRP B 878 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 878 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 878 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 878 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 878 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 878 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 878 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 878 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 878 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO C 658 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 960 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO C 961 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 961 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 961 " 0.036 5.00e-02 4.00e+02 ... (remaining 4199 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4945 2.78 - 3.31: 21816 3.31 - 3.84: 38267 3.84 - 4.37: 42515 4.37 - 4.90: 74291 Nonbonded interactions: 181834 Sorted by model distance: nonbonded pdb=" OD1 ASN B 79 " pdb=" OH TYR B 97 " model vdw 2.250 3.040 nonbonded pdb=" OE2 GLU B 275 " pdb=" OG1 THR B 277 " model vdw 2.287 3.040 nonbonded pdb=" O ARG C 112 " pdb=" OG1 THR C 116 " model vdw 2.295 3.040 nonbonded pdb=" O SER C 459 " pdb=" OG SER C 459 " model vdw 2.296 3.040 nonbonded pdb=" OE1 GLN B 876 " pdb=" NE2 GLN B 879 " model vdw 2.304 3.120 ... (remaining 181829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.980 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.006 0.055 24215 Z= 0.271 Angle : 0.843 14.787 33028 Z= 0.454 Chirality : 0.050 0.235 3627 Planarity : 0.006 0.069 4202 Dihedral : 16.474 90.034 9152 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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 are not related in a simple way. whole: -1.62 (0.15), residues: 2844 helix: -0.11 (0.13), residues: 1422 sheet: -1.14 (0.34), residues: 262 loop : -2.26 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 77 TYR 0.022 0.002 TYR B 173 PHE 0.022 0.002 PHE D 546 TRP 0.050 0.002 TRP B 878 HIS 0.005 0.001 HIS C 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.27 (24215) covalent geometry : angle 0.84277 / 0.45 (33028) hydrogen bonds : bond 0.12517 / 8.46 ( 1080) hydrogen bonds : angle 5.72924 / 4.04 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.933 Fit side-chains REVERT: B 1140 TYR cc_start: 0.7388 (m-10) cc_final: 0.6911 (m-10) REVERT: C 345 LEU cc_start: 0.9277 (tp) cc_final: 0.9038 (tp) REVERT: C 639 ASP cc_start: 0.7607 (t0) cc_final: 0.7398 (t70) REVERT: C 643 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7417 (tm-30) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1539 time to fit residues: 48.8872 Evaluate side-chains 139 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN B 162 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 HIS C 162 GLN C 572 ASN C 699 GLN C 793 ASN C 850 GLN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.102211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.077702 restraints weight = 55396.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.080038 restraints weight = 29490.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081573 restraints weight = 19636.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082492 restraints weight = 15144.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.083141 restraints weight = 12894.945| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24215 Z= 0.127 Angle : 0.592 8.684 33028 Z= 0.306 Chirality : 0.041 0.169 3627 Planarity : 0.004 0.056 4202 Dihedral : 12.687 71.764 3590 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.45 % Allowed : 5.82 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.79 (0.16), residues: 2844 helix: 0.70 (0.14), residues: 1418 sheet: -0.88 (0.34), residues: 255 loop : -2.00 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 17 TYR 0.016 0.001 TYR D 108 PHE 0.044 0.001 PHE D 386 TRP 0.028 0.001 TRP B 878 HIS 0.005 0.001 HIS B1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (24215) covalent geometry : angle 0.59201 / 0.31 (33028) hydrogen bonds : bond 0.04766 / 3.09 ( 1080) hydrogen bonds : angle 4.51232 / 3.20 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.787 Fit side-chains REVERT: B 257 PHE cc_start: 0.7288 (t80) cc_final: 0.7054 (t80) REVERT: B 259 ARG cc_start: 0.7246 (ttt180) cc_final: 0.6941 (ttt180) REVERT: B 325 ASP cc_start: 0.8021 (p0) cc_final: 0.7795 (p0) REVERT: B 426 ASP cc_start: 0.8082 (t0) cc_final: 0.7636 (m-30) REVERT: B 1077 TYR cc_start: 0.7653 (m-80) cc_final: 0.7373 (m-80) REVERT: C 267 HIS cc_start: 0.5055 (p-80) cc_final: 0.4843 (p-80) REVERT: C 345 LEU cc_start: 0.9520 (tp) cc_final: 0.9253 (tp) REVERT: C 639 ASP cc_start: 0.7895 (t0) cc_final: 0.7513 (t70) REVERT: C 643 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7173 (tm-30) REVERT: C 978 MET cc_start: 0.8590 (tpp) cc_final: 0.8171 (tpp) outliers start: 11 outliers final: 8 residues processed: 171 average time/residue: 0.1286 time to fit residues: 37.1860 Evaluate side-chains 148 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 250 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 HIS B1103 GLN B1153 GLN C 6 HIS C 339 GLN C 522 HIS ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.099476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074016 restraints weight = 57479.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076275 restraints weight = 31874.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077767 restraints weight = 21764.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078724 restraints weight = 17012.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.079266 restraints weight = 14531.718| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24215 Z= 0.226 Angle : 0.648 10.819 33028 Z= 0.329 Chirality : 0.043 0.188 3627 Planarity : 0.005 0.055 4202 Dihedral : 12.793 74.701 3590 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.87 % Allowed : 9.95 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.61 (0.16), residues: 2844 helix: 0.96 (0.14), residues: 1425 sheet: -1.05 (0.34), residues: 247 loop : -2.02 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.013 0.002 TYR B1156 PHE 0.040 0.002 PHE D 386 TRP 0.022 0.001 TRP B 878 HIS 0.006 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (24215) covalent geometry : angle 0.64848 / 0.33 (33028) hydrogen bonds : bond 0.04916 / 3.23 ( 1080) hydrogen bonds : angle 4.48418 / 3.20 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.660 Fit side-chains REVERT: B 325 ASP cc_start: 0.8057 (p0) cc_final: 0.7839 (p0) REVERT: B 426 ASP cc_start: 0.8022 (t0) cc_final: 0.7555 (m-30) REVERT: B 1077 TYR cc_start: 0.7663 (m-80) cc_final: 0.7146 (m-80) REVERT: C 96 MET cc_start: 0.8784 (tpp) cc_final: 0.8527 (ttm) REVERT: C 234 ILE cc_start: 0.8316 (mt) cc_final: 0.8069 (tt) REVERT: C 345 LEU cc_start: 0.9567 (tp) cc_final: 0.9361 (tp) REVERT: C 639 ASP cc_start: 0.7990 (t0) cc_final: 0.7606 (t70) REVERT: C 643 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7130 (tm-30) REVERT: C 978 MET cc_start: 0.8684 (tpp) cc_final: 0.8329 (tpp) REVERT: C 1080 MET cc_start: 0.7025 (ppp) cc_final: 0.6253 (ptt) REVERT: D 269 ASP cc_start: 0.8812 (t0) cc_final: 0.8600 (t0) outliers start: 21 outliers final: 16 residues processed: 166 average time/residue: 0.1340 time to fit residues: 37.4146 Evaluate side-chains 155 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 812 HIS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 45 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 139 optimal weight: 0.0980 chunk 25 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 HIS ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.101897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077398 restraints weight = 55256.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.079705 restraints weight = 29711.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081225 restraints weight = 19916.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082190 restraints weight = 15379.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082785 restraints weight = 13057.418| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24215 Z= 0.112 Angle : 0.541 9.704 33028 Z= 0.277 Chirality : 0.040 0.160 3627 Planarity : 0.004 0.052 4202 Dihedral : 12.716 74.865 3590 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.95 % Allowed : 11.43 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2844 helix: 1.32 (0.14), residues: 1411 sheet: -0.94 (0.34), residues: 253 loop : -1.79 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.012 0.001 TYR D 108 PHE 0.025 0.001 PHE D 386 TRP 0.013 0.001 TRP B 878 HIS 0.004 0.001 HIS B1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (24215) covalent geometry : angle 0.54068 / 0.28 (33028) hydrogen bonds : bond 0.04023 / 2.62 ( 1080) hydrogen bonds : angle 4.16710 / 2.97 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.891 Fit side-chains REVERT: B 259 ARG cc_start: 0.7342 (ttt180) cc_final: 0.7001 (ttt180) REVERT: B 325 ASP cc_start: 0.7981 (p0) cc_final: 0.7727 (p0) REVERT: B 426 ASP cc_start: 0.8214 (t0) cc_final: 0.7814 (m-30) REVERT: B 1077 TYR cc_start: 0.7621 (m-80) cc_final: 0.7131 (m-80) REVERT: C 96 MET cc_start: 0.8781 (tpp) cc_final: 0.8219 (ttm) REVERT: C 267 HIS cc_start: 0.5015 (p-80) cc_final: 0.4711 (p-80) REVERT: C 639 ASP cc_start: 0.7902 (t0) cc_final: 0.7504 (t70) REVERT: C 643 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7017 (tm-30) REVERT: C 1080 MET cc_start: 0.6899 (ppp) cc_final: 0.6184 (ptp) REVERT: D 19 LEU cc_start: 0.7855 (tt) cc_final: 0.7648 (tt) REVERT: D 269 ASP cc_start: 0.8785 (t0) cc_final: 0.8499 (t0) REVERT: D 497 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8134 (m-30) outliers start: 23 outliers final: 14 residues processed: 180 average time/residue: 0.1317 time to fit residues: 40.5007 Evaluate side-chains 159 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 812 HIS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 176 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 127 optimal weight: 0.0170 chunk 276 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 214 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 GLN B 812 HIS D 387 GLN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.102171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077585 restraints weight = 55199.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.079908 restraints weight = 29847.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081443 restraints weight = 19941.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082418 restraints weight = 15369.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083003 restraints weight = 13017.298| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 24215 Z= 0.113 Angle : 0.537 10.033 33028 Z= 0.274 Chirality : 0.039 0.176 3627 Planarity : 0.004 0.048 4202 Dihedral : 12.650 75.373 3590 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.91 % Allowed : 12.46 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.06 (0.16), residues: 2844 helix: 1.43 (0.14), residues: 1410 sheet: -0.87 (0.33), residues: 280 loop : -1.75 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 728 TYR 0.017 0.001 TYR B 648 PHE 0.020 0.001 PHE D 386 TRP 0.011 0.001 TRP B 878 HIS 0.021 0.001 HIS B 812 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (24215) covalent geometry : angle 0.53718 / 0.27 (33028) hydrogen bonds : bond 0.03916 / 2.54 ( 1080) hydrogen bonds : angle 4.09915 / 2.92 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: B 325 ASP cc_start: 0.7991 (p0) cc_final: 0.7737 (p0) REVERT: B 426 ASP cc_start: 0.8189 (t0) cc_final: 0.7871 (m-30) REVERT: B 1077 TYR cc_start: 0.7538 (m-80) cc_final: 0.7056 (m-80) REVERT: C 96 MET cc_start: 0.8785 (tpp) cc_final: 0.8268 (ttm) REVERT: C 267 HIS cc_start: 0.5004 (p-80) cc_final: 0.4734 (p-80) REVERT: C 639 ASP cc_start: 0.7905 (t0) cc_final: 0.7515 (t70) REVERT: C 643 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7089 (tm-30) REVERT: C 978 MET cc_start: 0.8679 (tpp) cc_final: 0.8426 (tpp) REVERT: C 1080 MET cc_start: 0.6863 (ppp) cc_final: 0.6199 (ptp) REVERT: D 19 LEU cc_start: 0.7793 (tt) cc_final: 0.7478 (tt) REVERT: D 269 ASP cc_start: 0.8800 (t0) cc_final: 0.8466 (t0) REVERT: D 497 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8105 (m-30) outliers start: 22 outliers final: 15 residues processed: 172 average time/residue: 0.1321 time to fit residues: 38.9613 Evaluate side-chains 157 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 26 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 257 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 HIS ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.100269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.075730 restraints weight = 55980.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.077969 restraints weight = 30694.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079464 restraints weight = 20811.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080416 restraints weight = 16088.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.081019 restraints weight = 13699.200| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24215 Z= 0.190 Angle : 0.589 10.922 33028 Z= 0.299 Chirality : 0.041 0.171 3627 Planarity : 0.004 0.053 4202 Dihedral : 12.652 75.880 3590 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.24 % Allowed : 13.29 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.15 (0.16), residues: 2844 helix: 1.39 (0.14), residues: 1419 sheet: -0.96 (0.33), residues: 280 loop : -1.83 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 25 TYR 0.017 0.001 TYR D 108 PHE 0.034 0.001 PHE B 257 TRP 0.020 0.001 TRP B 878 HIS 0.005 0.001 HIS D 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (24215) covalent geometry : angle 0.58876 / 0.30 (33028) hydrogen bonds : bond 0.04310 / 2.82 ( 1080) hydrogen bonds : angle 4.22624 / 3.03 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 259 ARG cc_start: 0.7612 (ttt180) cc_final: 0.7359 (ttt180) REVERT: B 325 ASP cc_start: 0.7983 (p0) cc_final: 0.7778 (p0) REVERT: B 426 ASP cc_start: 0.8270 (t0) cc_final: 0.7812 (m-30) REVERT: B 504 MET cc_start: 0.7310 (mmm) cc_final: 0.7083 (mmm) REVERT: B 888 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8082 (pp) REVERT: B 1077 TYR cc_start: 0.7494 (m-80) cc_final: 0.7027 (m-80) REVERT: C 96 MET cc_start: 0.8796 (tpp) cc_final: 0.8414 (ttm) REVERT: C 267 HIS cc_start: 0.5193 (p-80) cc_final: 0.4758 (p-80) REVERT: C 639 ASP cc_start: 0.7879 (t0) cc_final: 0.7539 (t70) REVERT: C 643 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7086 (tm-30) REVERT: C 978 MET cc_start: 0.8767 (tpp) cc_final: 0.8456 (tpp) REVERT: C 1080 MET cc_start: 0.6804 (ppp) cc_final: 0.6342 (ptt) REVERT: D 269 ASP cc_start: 0.8829 (t0) cc_final: 0.8480 (t0) REVERT: D 497 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8091 (m-30) outliers start: 30 outliers final: 23 residues processed: 167 average time/residue: 0.1504 time to fit residues: 42.7615 Evaluate side-chains 170 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 184 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 284 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074412 restraints weight = 56062.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.076631 restraints weight = 30578.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078089 restraints weight = 20643.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079023 restraints weight = 16014.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.079583 restraints weight = 13607.259| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24215 Z= 0.235 Angle : 0.639 12.156 33028 Z= 0.323 Chirality : 0.043 0.326 3627 Planarity : 0.004 0.053 4202 Dihedral : 12.686 76.232 3590 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.44 % Allowed : 13.58 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.28 (0.16), residues: 2844 helix: 1.28 (0.14), residues: 1411 sheet: -1.04 (0.33), residues: 264 loop : -1.87 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 734 TYR 0.012 0.002 TYR B 514 PHE 0.025 0.002 PHE B 257 TRP 0.023 0.001 TRP B 878 HIS 0.005 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (24215) covalent geometry : angle 0.63948 / 0.32 (33028) hydrogen bonds : bond 0.04634 / 3.06 ( 1080) hydrogen bonds : angle 4.37418 / 3.13 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: B 259 ARG cc_start: 0.7475 (ttt180) cc_final: 0.7159 (ttt180) REVERT: B 325 ASP cc_start: 0.8020 (p0) cc_final: 0.7820 (p0) REVERT: B 504 MET cc_start: 0.7398 (mmm) cc_final: 0.7185 (mmm) REVERT: B 888 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8038 (pp) REVERT: B 1077 TYR cc_start: 0.7524 (m-80) cc_final: 0.6948 (m-80) REVERT: C 96 MET cc_start: 0.8746 (tpp) cc_final: 0.8410 (ttm) REVERT: C 639 ASP cc_start: 0.7917 (t0) cc_final: 0.7630 (t70) REVERT: C 643 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7154 (tm-30) REVERT: C 978 MET cc_start: 0.8797 (tpp) cc_final: 0.8475 (tpp) REVERT: C 1080 MET cc_start: 0.6727 (ppp) cc_final: 0.6510 (ptt) REVERT: D 269 ASP cc_start: 0.8852 (t0) cc_final: 0.8548 (t0) REVERT: D 497 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7947 (m-30) outliers start: 35 outliers final: 27 residues processed: 174 average time/residue: 0.1500 time to fit residues: 44.2539 Evaluate side-chains 166 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 863 GLU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 192 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.076601 restraints weight = 55234.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.078899 restraints weight = 29830.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080416 restraints weight = 20000.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.081375 restraints weight = 15376.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081940 restraints weight = 13049.302| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24215 Z= 0.118 Angle : 0.553 11.688 33028 Z= 0.282 Chirality : 0.040 0.201 3627 Planarity : 0.004 0.052 4202 Dihedral : 12.614 76.413 3590 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.49 % Allowed : 14.03 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2844 helix: 1.49 (0.14), residues: 1407 sheet: -0.90 (0.33), residues: 278 loop : -1.73 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.014 0.001 TYR B 200 PHE 0.043 0.001 PHE B 257 TRP 0.023 0.001 TRP B 878 HIS 0.004 0.001 HIS B1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (24215) covalent geometry : angle 0.55330 / 0.28 (33028) hydrogen bonds : bond 0.04007 / 2.62 ( 1080) hydrogen bonds : angle 4.12819 / 2.96 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 259 ARG cc_start: 0.7469 (ttt180) cc_final: 0.7189 (ttt180) REVERT: B 325 ASP cc_start: 0.7979 (p0) cc_final: 0.7733 (p0) REVERT: B 589 GLU cc_start: 0.7374 (tt0) cc_final: 0.7068 (tm-30) REVERT: B 714 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7924 (m90) REVERT: B 888 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8086 (pp) REVERT: B 1077 TYR cc_start: 0.7546 (m-80) cc_final: 0.7328 (m-80) REVERT: C 96 MET cc_start: 0.8779 (tpp) cc_final: 0.8446 (ttm) REVERT: C 267 HIS cc_start: 0.4779 (p-80) cc_final: 0.4326 (p-80) REVERT: C 639 ASP cc_start: 0.7861 (t0) cc_final: 0.7569 (t70) REVERT: C 643 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7139 (tm-30) REVERT: C 978 MET cc_start: 0.8681 (tpp) cc_final: 0.8352 (tpp) REVERT: C 1080 MET cc_start: 0.6671 (ppp) cc_final: 0.6421 (ptt) REVERT: D 59 GLU cc_start: 0.2669 (OUTLIER) cc_final: 0.2418 (pm20) REVERT: D 269 ASP cc_start: 0.8851 (t0) cc_final: 0.8544 (t0) REVERT: D 497 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7921 (m-30) outliers start: 36 outliers final: 23 residues processed: 179 average time/residue: 0.1449 time to fit residues: 43.9879 Evaluate side-chains 166 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 714 HIS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 273 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 256 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN B 765 GLN B 879 GLN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.099715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075264 restraints weight = 55933.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.077512 restraints weight = 30423.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.079014 restraints weight = 20544.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.079974 restraints weight = 15840.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080505 restraints weight = 13461.638| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24215 Z= 0.185 Angle : 0.601 12.415 33028 Z= 0.304 Chirality : 0.041 0.187 3627 Planarity : 0.004 0.053 4202 Dihedral : 12.609 76.615 3590 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.28 % Allowed : 14.57 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.08 (0.16), residues: 2844 helix: 1.44 (0.14), residues: 1411 sheet: -0.88 (0.34), residues: 262 loop : -1.78 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 808 TYR 0.017 0.001 TYR B 200 PHE 0.039 0.001 PHE B 257 TRP 0.024 0.001 TRP B 878 HIS 0.004 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (24215) covalent geometry : angle 0.60126 / 0.30 (33028) hydrogen bonds : bond 0.04273 / 2.81 ( 1080) hydrogen bonds : angle 4.21954 / 3.03 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: B 259 ARG cc_start: 0.7411 (ttt180) cc_final: 0.7108 (ttt180) REVERT: B 325 ASP cc_start: 0.7991 (p0) cc_final: 0.7788 (p0) REVERT: B 589 GLU cc_start: 0.7374 (tt0) cc_final: 0.7073 (tm-30) REVERT: B 714 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.7960 (m90) REVERT: B 888 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8070 (pp) REVERT: B 1077 TYR cc_start: 0.7577 (m-80) cc_final: 0.7335 (m-80) REVERT: C 96 MET cc_start: 0.8774 (tpp) cc_final: 0.8385 (ttm) REVERT: C 267 HIS cc_start: 0.4903 (p-80) cc_final: 0.4394 (p-80) REVERT: C 639 ASP cc_start: 0.7897 (t0) cc_final: 0.7613 (t70) REVERT: C 643 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7137 (tm-30) REVERT: C 978 MET cc_start: 0.8742 (tpp) cc_final: 0.8417 (tpp) REVERT: D 269 ASP cc_start: 0.8882 (t0) cc_final: 0.8582 (t0) REVERT: D 497 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7929 (m-30) outliers start: 31 outliers final: 25 residues processed: 171 average time/residue: 0.1483 time to fit residues: 42.3311 Evaluate side-chains 169 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 714 HIS Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1114 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 237 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 250 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 GLN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076012 restraints weight = 55552.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078286 restraints weight = 30042.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.079760 restraints weight = 20218.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080723 restraints weight = 15645.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.081275 restraints weight = 13261.631| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24215 Z= 0.148 Angle : 0.584 12.887 33028 Z= 0.295 Chirality : 0.041 0.241 3627 Planarity : 0.004 0.053 4202 Dihedral : 12.586 77.142 3590 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.16 % Allowed : 14.73 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2844 helix: 1.44 (0.14), residues: 1418 sheet: -0.82 (0.34), residues: 262 loop : -1.77 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 734 TYR 0.018 0.001 TYR B 200 PHE 0.040 0.001 PHE D 386 TRP 0.025 0.001 TRP B 878 HIS 0.004 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (24215) covalent geometry : angle 0.58357 / 0.29 (33028) hydrogen bonds : bond 0.04118 / 2.70 ( 1080) hydrogen bonds : angle 4.14735 / 2.98 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 259 ARG cc_start: 0.7413 (ttt180) cc_final: 0.7114 (ttt180) REVERT: B 325 ASP cc_start: 0.7965 (p0) cc_final: 0.7755 (p0) REVERT: B 504 MET cc_start: 0.7375 (mmm) cc_final: 0.7083 (tpt) REVERT: B 589 GLU cc_start: 0.7376 (tt0) cc_final: 0.7070 (tm-30) REVERT: B 888 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8106 (pp) REVERT: B 1056 MET cc_start: 0.7914 (tpt) cc_final: 0.7696 (tpt) REVERT: B 1077 TYR cc_start: 0.7596 (m-80) cc_final: 0.7352 (m-80) REVERT: C 96 MET cc_start: 0.8786 (tpp) cc_final: 0.8426 (ttm) REVERT: C 267 HIS cc_start: 0.4834 (p-80) cc_final: 0.4334 (p-80) REVERT: C 639 ASP cc_start: 0.7880 (t0) cc_final: 0.7594 (t70) REVERT: C 643 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7151 (tm-30) REVERT: D 59 GLU cc_start: 0.2673 (OUTLIER) cc_final: 0.2396 (pm20) REVERT: D 269 ASP cc_start: 0.8893 (t0) cc_final: 0.8600 (t0) REVERT: D 497 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7943 (m-30) outliers start: 28 outliers final: 25 residues processed: 168 average time/residue: 0.1464 time to fit residues: 41.6814 Evaluate side-chains 170 residues out of total 2423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1088 ILE Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain D residue 497 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 190 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.102037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.076834 restraints weight = 56406.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.079137 restraints weight = 31113.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080637 restraints weight = 21093.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.081630 restraints weight = 16496.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082250 restraints weight = 13959.365| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24215 Z= 0.113 Angle : 0.557 12.286 33028 Z= 0.281 Chirality : 0.040 0.191 3627 Planarity : 0.004 0.051 4202 Dihedral : 12.541 76.959 3590 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.07 % Allowed : 14.90 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2844 helix: 1.56 (0.14), residues: 1418 sheet: -0.71 (0.33), residues: 276 loop : -1.70 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1015 TYR 0.020 0.001 TYR B 200 PHE 0.046 0.001 PHE D 386 TRP 0.024 0.001 TRP B 878 HIS 0.004 0.001 HIS B1134 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (24215) covalent geometry : angle 0.55713 / 0.28 (33028) hydrogen bonds : bond 0.03836 / 2.49 ( 1080) hydrogen bonds : angle 4.02865 / 2.90 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.46 seconds wall clock time: 57 minutes 32.93 seconds (3452.93 seconds total)