Starting phenix.real_space_refine on Fri Aug 7 21:03:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b1u_15805/08_2026/8b1u_15805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b1u_15805/08_2026/8b1u_15805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2026/8b1u_15805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2026/8b1u_15805.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2026/8b1u_15805.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2026/8b1u_15805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2026/8b1u_15805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2026/8b1u_15805.map" } resolution = 3.8 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 53 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 15088 2.51 5 N 4249 2.21 5 O 4632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24127 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 9145 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 1 Chain: "C" Number of atoms: 8738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8738 Classifications: {'peptide': 1080} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1014} Chain breaks: 1 Chain: "D" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4644 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 25, 'TRANS': 575} Chain breaks: 1 Chain: "X" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1035 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "A" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 533 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.51, per 1000 atoms: 0.19 Number of scatterers: 24127 At special positions: 0 Unit cell: (154.76, 152.64, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 53 15.00 Mg 1 11.99 O 4632 8.00 N 4249 7.00 C 15088 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: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5446 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 18 sheets defined 56.5% alpha, 10.2% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.722A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' 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 121 removed outlier: 3.513A pdb=" N ALA B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.644A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.517A pdb=" N ASP B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 Processing helix chain 'B' and resid 241 through 250 removed outlier: 4.254A pdb=" N ALA B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.781A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.859A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.692A pdb=" N ARG B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.775A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 510 through 535 removed outlier: 3.804A pdb=" N ARG B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.783A pdb=" N LEU B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 4.073A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 624 through 632 removed outlier: 3.594A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 656 removed outlier: 3.601A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 669 Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 679 through 701 removed outlier: 4.003A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 3.775A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 Processing helix chain 'B' and resid 832 through 835 Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 849 through 861 Processing helix chain 'B' and resid 905 through 911 Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 948 through 961 removed outlier: 3.543A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 985 through 1000 removed outlier: 4.438A pdb=" N VAL B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 4.659A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1050 Processing helix chain 'B' and resid 1089 through 1093 Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1106 through 1126 removed outlier: 4.083A pdb=" N GLN B1110 " --> pdb=" O ARG B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1161 through 1174 Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.059A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.509A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 103 removed outlier: 3.737A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 115 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.806A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.595A 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: 4.749A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 297 through 304 removed outlier: 3.814A pdb=" N TRP C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.754A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.518A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 429 removed outlier: 3.668A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix removed outlier: 3.691A pdb=" N ALA C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.502A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 removed outlier: 4.105A pdb=" N VAL C 476 " --> pdb=" O ALA C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.509A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.838A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 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 removed outlier: 3.579A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 removed outlier: 3.505A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 604 through 626 removed outlier: 4.353A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 646 removed outlier: 3.777A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.597A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 834 through 843 removed outlier: 3.916A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 874 through 890 removed outlier: 3.798A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 905 removed outlier: 3.890A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 935 removed outlier: 3.594A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 927 " --> pdb=" O GLU C 923 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 991 Processing helix chain 'C' and resid 1012 through 1033 Processing helix chain 'C' and resid 1040 through 1049 Processing helix chain 'C' and resid 1060 through 1077 Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 3.569A pdb=" N ARG C1092 " --> pdb=" O ILE C1088 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1120 Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.732A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 48 removed outlier: 3.575A pdb=" N THR D 36 " --> pdb=" O HIS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 removed outlier: 4.911A pdb=" N SER D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.597A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 removed outlier: 3.544A pdb=" N CYS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) 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 removed outlier: 3.625A pdb=" N GLN D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.505A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.862A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 322 through 334 Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 365 through 377 Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 400 through 424 removed outlier: 4.831A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.739A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.725A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.554A pdb=" N SER D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.732A pdb=" N ASN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 40 through 66 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.417A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR B 441 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 20 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE B 127 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.436A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA4, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.447A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 737 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N SER B 814 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 752 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N GLY B 816 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 754 " --> pdb=" O GLY B 816 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.361A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.361A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL B1058 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU B1029 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.192A pdb=" N GLU C 33 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.827A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.434A pdb=" N ALA C 438 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N THR C 663 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 442 through 443 removed outlier: 4.355A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 650 " --> pdb=" O ARG C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.711A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 963 through 968 removed outlier: 6.394A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.506A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.524A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 238 through 239 removed outlier: 8.939A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 171 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU D 355 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER D 170 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.749A pdb=" N PHE D 546 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ARG D 576 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS D 548 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER D 578 " --> pdb=" O HIS D 548 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA D 550 " --> pdb=" O SER D 578 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR D 580 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE D 552 " --> pdb=" O TYR D 580 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.768A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 6.28 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7168 1.34 - 1.45: 3901 1.45 - 1.57: 13403 1.57 - 1.69: 104 1.69 - 1.81: 174 Bond restraints: 24750 Sorted by residual: bond pdb=" O3A ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C3' DG X 23 " pdb=" C2' DG X 23 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.45e+01 bond pdb=" O5' ANP B1501 " pdb=" PA ANP B1501 " ideal model delta sigma weight residual 1.655 1.584 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C3' DG X 56 " pdb=" C2' DG X 56 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 24745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 33744 3.41 - 6.81: 44 6.81 - 10.22: 4 10.22 - 13.62: 2 13.62 - 17.03: 1 Bond angle restraints: 33795 Sorted by residual: angle pdb=" PB ANP B1501 " pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 126.95 109.92 17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" N3 DT X 15 " pdb=" C4 DT X 15 " pdb=" O4 DT X 15 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT X 63 " pdb=" C4 DT X 63 " pdb=" O4 DT X 63 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT X 27 " pdb=" C4 DT X 27 " pdb=" O4 DT X 27 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT X 9 " pdb=" C4 DT X 9 " pdb=" O4 DT X 9 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 33790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 13895 17.67 - 35.35: 601 35.35 - 53.02: 227 53.02 - 70.70: 77 70.70 - 88.37: 5 Dihedral angle restraints: 14805 sinusoidal: 6403 harmonic: 8402 Sorted by residual: dihedral pdb=" CA ASN B1003 " pdb=" C ASN B1003 " pdb=" N GLU B1004 " pdb=" CA GLU B1004 " ideal model delta harmonic sigma weight residual -180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR D 108 " pdb=" C TYR D 108 " pdb=" N LEU D 109 " pdb=" CA LEU D 109 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ASP C 484 " pdb=" CB ASP C 484 " pdb=" CG ASP C 484 " pdb=" OD1 ASP C 484 " ideal model delta sinusoidal sigma weight residual -30.00 -85.10 55.10 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 14802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3208 0.052 - 0.104: 437 0.104 - 0.155: 63 0.155 - 0.207: 1 0.207 - 0.259: 1 Chirality restraints: 3710 Sorted by residual: chirality pdb=" C3' ANP B1501 " pdb=" C2' ANP B1501 " pdb=" C4' ANP B1501 " pdb=" O3' ANP B1501 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU C 323 " pdb=" CB LEU C 323 " pdb=" CD1 LEU C 323 " pdb=" CD2 LEU C 323 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 3707 not shown) Planarity restraints: 4257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO C 658 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 50 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 51 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 381 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO C 382 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " -0.019 5.00e-02 4.00e+02 ... (remaining 4254 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 689 2.72 - 3.26: 23718 3.26 - 3.81: 38567 3.81 - 4.35: 47298 4.35 - 4.90: 79849 Nonbonded interactions: 190121 Sorted by model distance: nonbonded pdb=" OG1 THR B 30 " pdb="MG MG B1502 " model vdw 2.172 2.170 nonbonded pdb=" O2G ANP B1501 " pdb="MG MG B1502 " model vdw 2.202 2.170 nonbonded pdb=" OG SER B1090 " pdb=" OE1 GLN B1153 " model vdw 2.215 3.040 nonbonded pdb=" O ASN B 889 " pdb=" NE2 GLN C 800 " model vdw 2.237 3.120 nonbonded pdb=" O ALA B 361 " pdb=" OG SER B 364 " model vdw 2.250 3.040 ... (remaining 190116 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: 1.140 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.020 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.003 0.143 24750 Z= 0.206 Angle : 0.535 17.029 33795 Z= 0.365 Chirality : 0.036 0.259 3710 Planarity : 0.003 0.053 4257 Dihedral : 12.090 88.373 9359 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.08 % Favored : 98.89 % Rotamer: Outliers : 1.51 % Allowed : 3.06 % Favored : 95.43 % 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: -0.66 (0.14), residues: 2872 helix: 0.05 (0.12), residues: 1493 sheet: -0.51 (0.27), residues: 296 loop : -0.94 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1106 TYR 0.019 0.001 TYR B1111 PHE 0.009 0.001 PHE A 46 TRP 0.011 0.001 TRP B 652 HIS 0.002 0.000 HIS B 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.21 (24750) covalent geometry : angle 0.53507 / 0.36 (33795) hydrogen bonds : bond 0.15269 / 10.54 ( 1195) hydrogen bonds : angle 5.47088 / 3.86 ( 3447) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 652 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.8491 (mmm) cc_final: 0.8136 (mmm) REVERT: B 960 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7904 (tp30) REVERT: C 252 LYS cc_start: 0.7660 (mttt) cc_final: 0.7434 (pptt) REVERT: C 697 MET cc_start: 0.8153 (mtp) cc_final: 0.7933 (mtp) REVERT: C 897 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8287 (mt) REVERT: C 941 MET cc_start: 0.8006 (ptt) cc_final: 0.7347 (ptt) REVERT: C 955 TRP cc_start: 0.7550 (m100) cc_final: 0.7197 (m100) REVERT: C 973 SER cc_start: 0.7689 (p) cc_final: 0.6905 (t) REVERT: C 1035 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8346 (tp) REVERT: C 1054 ASN cc_start: 0.8275 (m-40) cc_final: 0.7669 (p0) REVERT: C 1079 MET cc_start: 0.7984 (ptm) cc_final: 0.7756 (ptp) REVERT: C 1086 ASP cc_start: 0.6915 (t0) cc_final: 0.6639 (t0) REVERT: A 9 ASP cc_start: 0.7536 (p0) cc_final: 0.7305 (p0) REVERT: A 47 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7704 (ttp80) outliers start: 37 outliers final: 4 residues processed: 676 average time/residue: 0.1858 time to fit residues: 187.1284 Evaluate side-chains 262 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 256 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN B 181 GLN B 458 ASN B 484 ASN B 624 ASN B 769 HIS B 835 GLN B 879 GLN B1018 GLN B1072 HIS ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 HIS B1161 ASN C 87 ASN C 137 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 336 HIS C 390 HIS C 448 HIS C 510 ASN C 739 ASN C 759 HIS C 979 GLN D 50 HIS D 247 GLN D 256 HIS D 469 HIS A 63 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.102880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081992 restraints weight = 61219.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.083977 restraints weight = 36644.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.085399 restraints weight = 23584.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.085511 restraints weight = 18106.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085595 restraints weight = 17614.757| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 24750 Z= 0.242 Angle : 0.699 11.007 33795 Z= 0.361 Chirality : 0.044 0.215 3710 Planarity : 0.005 0.053 4257 Dihedral : 13.583 87.505 3733 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.98 % Allowed : 10.61 % Favored : 86.41 % 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: 0.39 (0.15), residues: 2872 helix: 1.00 (0.13), residues: 1511 sheet: -0.23 (0.27), residues: 304 loop : -0.55 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 466 TYR 0.026 0.002 TYR A 30 PHE 0.028 0.002 PHE C 840 TRP 0.018 0.002 TRP B 652 HIS 0.008 0.001 HIS B1072 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (24750) covalent geometry : angle 0.69931 / 0.36 (33795) hydrogen bonds : bond 0.04884 / 3.28 ( 1195) hydrogen bonds : angle 4.54853 / 3.21 ( 3447) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 254 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: B 385 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6950 (mm-30) REVERT: B 518 MET cc_start: 0.8657 (mmm) cc_final: 0.8267 (mmm) REVERT: B 595 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6830 (mt-10) REVERT: B 620 MET cc_start: 0.7888 (ttm) cc_final: 0.7609 (ttm) REVERT: B 856 CYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8085 (t) REVERT: B 960 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7846 (tp30) REVERT: B 1169 ASP cc_start: 0.7784 (t70) cc_final: 0.7551 (t0) REVERT: C 897 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8748 (mp) REVERT: C 981 TRP cc_start: 0.8947 (t-100) cc_final: 0.8524 (t-100) REVERT: C 1054 ASN cc_start: 0.8381 (m-40) cc_final: 0.7687 (p0) REVERT: C 1079 MET cc_start: 0.8215 (ptm) cc_final: 0.7911 (ptp) REVERT: C 1086 ASP cc_start: 0.7884 (t0) cc_final: 0.7425 (t0) REVERT: D 83 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: D 314 CYS cc_start: 0.7636 (t) cc_final: 0.6969 (t) REVERT: A 9 ASP cc_start: 0.7928 (p0) cc_final: 0.7689 (p0) REVERT: A 61 ILE cc_start: 0.7733 (tp) cc_final: 0.7514 (pt) outliers start: 73 outliers final: 44 residues processed: 315 average time/residue: 0.1402 time to fit residues: 71.6553 Evaluate side-chains 251 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 15 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 284 optimal weight: 50.0000 chunk 189 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 278 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 291 GLN B 403 HIS B 484 ASN ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN B 971 ASN B1103 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 448 HIS C 688 GLN D 439 GLN D 542 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080660 restraints weight = 60782.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083191 restraints weight = 34961.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.083655 restraints weight = 22437.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.084040 restraints weight = 18518.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.084142 restraints weight = 17329.335| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 24750 Z= 0.195 Angle : 0.601 10.847 33795 Z= 0.311 Chirality : 0.040 0.177 3710 Planarity : 0.004 0.051 4257 Dihedral : 13.533 80.680 3729 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.98 % Allowed : 11.83 % Favored : 85.19 % 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: 0.79 (0.15), residues: 2872 helix: 1.37 (0.13), residues: 1517 sheet: -0.01 (0.27), residues: 305 loop : -0.47 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 292 TYR 0.024 0.002 TYR B1111 PHE 0.021 0.002 PHE B1172 TRP 0.016 0.001 TRP C 574 HIS 0.008 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (24750) covalent geometry : angle 0.60064 / 0.31 (33795) hydrogen bonds : bond 0.04604 / 3.09 ( 1195) hydrogen bonds : angle 4.27507 / 3.03 ( 3447) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 209 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 385 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7104 (mm-30) REVERT: B 595 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7135 (mt-10) REVERT: B 960 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7800 (tp30) REVERT: B 1002 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7576 (mm) REVERT: B 1169 ASP cc_start: 0.7696 (t70) cc_final: 0.7492 (t0) REVERT: C 667 MET cc_start: 0.8467 (mmp) cc_final: 0.8195 (mmt) REVERT: C 927 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8819 (tt) REVERT: C 981 TRP cc_start: 0.8991 (t-100) cc_final: 0.8596 (t-100) REVERT: C 1054 ASN cc_start: 0.8491 (m-40) cc_final: 0.7665 (p0) REVERT: C 1079 MET cc_start: 0.8151 (ptm) cc_final: 0.7830 (ptp) REVERT: C 1080 MET cc_start: 0.7556 (mpp) cc_final: 0.7315 (mpp) REVERT: C 1086 ASP cc_start: 0.7908 (t0) cc_final: 0.7477 (t0) REVERT: D 83 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: D 279 MET cc_start: 0.9153 (tpt) cc_final: 0.8640 (mmm) REVERT: D 444 LEU cc_start: 0.7984 (mp) cc_final: 0.7678 (tp) REVERT: A 28 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8344 (mtmm) REVERT: A 61 ILE cc_start: 0.7705 (tp) cc_final: 0.7474 (pt) outliers start: 73 outliers final: 46 residues processed: 269 average time/residue: 0.1400 time to fit residues: 62.4265 Evaluate side-chains 237 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 108 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 705 HIS ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.080597 restraints weight = 61004.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.083116 restraints weight = 38236.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084261 restraints weight = 22445.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084263 restraints weight = 18590.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.084429 restraints weight = 17968.909| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24750 Z= 0.152 Angle : 0.567 10.151 33795 Z= 0.290 Chirality : 0.039 0.284 3710 Planarity : 0.004 0.047 4257 Dihedral : 13.516 83.131 3729 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.90 % Allowed : 12.44 % Favored : 84.66 % 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: 1.01 (0.16), residues: 2872 helix: 1.55 (0.13), residues: 1519 sheet: 0.17 (0.28), residues: 306 loop : -0.41 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 298 TYR 0.022 0.001 TYR B1111 PHE 0.014 0.001 PHE C 840 TRP 0.014 0.001 TRP C 574 HIS 0.006 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24750) covalent geometry : angle 0.56662 / 0.29 (33795) hydrogen bonds : bond 0.04091 / 2.75 ( 1195) hydrogen bonds : angle 4.14376 / 2.94 ( 3447) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 204 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7627 (tm-30) REVERT: B 385 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7170 (mm-30) REVERT: B 1102 MET cc_start: 0.6671 (mmp) cc_final: 0.6439 (mmm) REVERT: C 667 MET cc_start: 0.8383 (mmp) cc_final: 0.8146 (mmt) REVERT: C 775 ARG cc_start: 0.7533 (tpp80) cc_final: 0.6932 (ttm-80) REVERT: C 853 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8501 (pp) REVERT: C 927 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8833 (tt) REVERT: C 981 TRP cc_start: 0.8970 (t-100) cc_final: 0.8517 (t-100) REVERT: C 1054 ASN cc_start: 0.8374 (m-40) cc_final: 0.7600 (p0) REVERT: C 1079 MET cc_start: 0.8010 (ptm) cc_final: 0.7612 (ptp) REVERT: C 1086 ASP cc_start: 0.7902 (t0) cc_final: 0.7493 (t0) REVERT: D 83 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: D 279 MET cc_start: 0.9235 (tpt) cc_final: 0.8872 (mmm) REVERT: A 28 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8210 (mtmm) REVERT: A 61 ILE cc_start: 0.7801 (tp) cc_final: 0.7575 (pt) outliers start: 71 outliers final: 44 residues processed: 265 average time/residue: 0.1369 time to fit residues: 60.1998 Evaluate side-chains 230 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 572 ARG Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 27 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 219 optimal weight: 0.0020 chunk 187 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 150 optimal weight: 0.0570 chunk 182 optimal weight: 0.9980 overall best weight: 0.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 594 GLN B 726 GLN B 879 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082135 restraints weight = 59953.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.085095 restraints weight = 37110.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085765 restraints weight = 21522.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.085895 restraints weight = 17748.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086065 restraints weight = 17347.158| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 24750 Z= 0.106 Angle : 0.528 10.109 33795 Z= 0.271 Chirality : 0.038 0.214 3710 Planarity : 0.003 0.049 4257 Dihedral : 13.457 83.625 3728 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.90 % Allowed : 12.44 % Favored : 84.66 % 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: 1.22 (0.16), residues: 2872 helix: 1.72 (0.13), residues: 1520 sheet: 0.41 (0.28), residues: 304 loop : -0.36 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1028 TYR 0.019 0.001 TYR B1111 PHE 0.013 0.001 PHE C 840 TRP 0.014 0.001 TRP C 574 HIS 0.003 0.001 HIS D 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (24750) covalent geometry : angle 0.52768 / 0.27 (33795) hydrogen bonds : bond 0.03654 / 2.46 ( 1195) hydrogen bonds : angle 3.98189 / 2.83 ( 3447) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 217 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 385 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7122 (mm-30) REVERT: B 1102 MET cc_start: 0.6806 (mmp) cc_final: 0.6569 (mmm) REVERT: C 667 MET cc_start: 0.8336 (mmp) cc_final: 0.8107 (mmt) REVERT: C 712 ASP cc_start: 0.8445 (m-30) cc_final: 0.7851 (t0) REVERT: C 853 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8412 (pp) REVERT: C 927 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8792 (tt) REVERT: C 1031 MET cc_start: 0.8400 (mmp) cc_final: 0.7910 (tpp) REVERT: C 1054 ASN cc_start: 0.8346 (m-40) cc_final: 0.7586 (p0) REVERT: C 1079 MET cc_start: 0.8061 (ptm) cc_final: 0.7725 (ptp) REVERT: C 1086 ASP cc_start: 0.7871 (t0) cc_final: 0.7471 (t0) REVERT: D 83 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 28 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8188 (mtmm) REVERT: A 61 ILE cc_start: 0.7799 (tp) cc_final: 0.7576 (pt) outliers start: 71 outliers final: 47 residues processed: 272 average time/residue: 0.1490 time to fit residues: 67.4086 Evaluate side-chains 245 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 195 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 141 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 179 optimal weight: 0.0170 chunk 139 optimal weight: 9.9990 chunk 180 optimal weight: 0.9980 overall best weight: 3.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 140 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 960 GLN ** D 300 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 = 0.3583 r_free = 0.3583 target = 0.101115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079629 restraints weight = 61304.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.082132 restraints weight = 37393.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083297 restraints weight = 22418.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083376 restraints weight = 18675.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.083574 restraints weight = 17956.377| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 24750 Z= 0.171 Angle : 0.572 12.894 33795 Z= 0.289 Chirality : 0.039 0.318 3710 Planarity : 0.004 0.047 4257 Dihedral : 13.454 84.053 3724 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.94 % Allowed : 13.46 % Favored : 83.60 % 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: 1.24 (0.16), residues: 2872 helix: 1.76 (0.14), residues: 1516 sheet: 0.36 (0.28), residues: 303 loop : -0.35 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 668 TYR 0.022 0.001 TYR B1111 PHE 0.032 0.002 PHE C 840 TRP 0.014 0.001 TRP B 652 HIS 0.007 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (24750) covalent geometry : angle 0.57212 / 0.29 (33795) hydrogen bonds : bond 0.03953 / 2.66 ( 1195) hydrogen bonds : angle 4.06145 / 2.88 ( 3447) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8673 (tt) cc_final: 0.8447 (tp) REVERT: B 136 MET cc_start: 0.8411 (tpp) cc_final: 0.8040 (tpp) REVERT: B 342 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 550 ARG cc_start: 0.6972 (mpp80) cc_final: 0.6713 (mpp80) REVERT: B 824 ARG cc_start: 0.5791 (OUTLIER) cc_final: 0.5467 (ptp90) REVERT: B 1171 MET cc_start: 0.9154 (tmm) cc_final: 0.8883 (ppp) REVERT: C 1 MET cc_start: 0.8063 (tpp) cc_final: 0.7464 (tpt) REVERT: C 667 MET cc_start: 0.8487 (mmp) cc_final: 0.8196 (mmt) REVERT: C 853 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8414 (pp) REVERT: C 927 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8812 (tt) REVERT: C 1054 ASN cc_start: 0.8541 (m-40) cc_final: 0.7661 (p0) REVERT: C 1086 ASP cc_start: 0.7954 (t0) cc_final: 0.7522 (t0) REVERT: D 83 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: D 579 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8644 (tt) REVERT: A 28 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8340 (mtmm) REVERT: A 61 ILE cc_start: 0.7787 (tp) cc_final: 0.7568 (pt) outliers start: 72 outliers final: 50 residues processed: 260 average time/residue: 0.1547 time to fit residues: 65.3036 Evaluate side-chains 241 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 186 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 968 VAL Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 228 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 209 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 31 optimal weight: 0.0060 chunk 233 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN D 300 GLN D 523 GLN A 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.082884 restraints weight = 61263.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084518 restraints weight = 39386.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085437 restraints weight = 26641.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.085753 restraints weight = 21329.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.086083 restraints weight = 20377.622| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24750 Z= 0.103 Angle : 0.548 16.448 33795 Z= 0.275 Chirality : 0.038 0.180 3710 Planarity : 0.003 0.050 4257 Dihedral : 13.385 84.513 3724 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.57 % Allowed : 13.63 % Favored : 83.80 % 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: 1.45 (0.16), residues: 2872 helix: 1.92 (0.14), residues: 1510 sheet: 0.50 (0.29), residues: 304 loop : -0.27 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 23 TYR 0.019 0.001 TYR A 30 PHE 0.020 0.001 PHE C 840 TRP 0.013 0.001 TRP B 652 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (24750) covalent geometry : angle 0.54841 / 0.27 (33795) hydrogen bonds : bond 0.03438 / 2.31 ( 1195) hydrogen bonds : angle 3.90778 / 2.77 ( 3447) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.8293 (tpp) cc_final: 0.7951 (tpp) REVERT: B 342 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7482 (tm-30) REVERT: B 824 ARG cc_start: 0.5646 (OUTLIER) cc_final: 0.5362 (ptp90) REVERT: B 1102 MET cc_start: 0.6510 (mmp) cc_final: 0.6134 (mmm) REVERT: C 1 MET cc_start: 0.7896 (tpp) cc_final: 0.7390 (tpt) REVERT: C 594 MET cc_start: 0.8757 (mmm) cc_final: 0.8522 (mmm) REVERT: C 712 ASP cc_start: 0.8419 (m-30) cc_final: 0.7817 (t0) REVERT: C 775 ARG cc_start: 0.7429 (tpp80) cc_final: 0.6817 (ttm-80) REVERT: C 853 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8410 (pp) REVERT: C 927 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8747 (tt) REVERT: C 1054 ASN cc_start: 0.8361 (m-40) cc_final: 0.7607 (p0) REVERT: C 1086 ASP cc_start: 0.7872 (t0) cc_final: 0.7482 (t0) REVERT: D 83 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: D 184 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8399 (tp) REVERT: D 322 THR cc_start: 0.4438 (OUTLIER) cc_final: 0.4227 (p) REVERT: A 28 LYS cc_start: 0.8442 (mtmm) cc_final: 0.8114 (mtmm) REVERT: A 61 ILE cc_start: 0.7821 (tp) cc_final: 0.7594 (pt) outliers start: 63 outliers final: 42 residues processed: 258 average time/residue: 0.1497 time to fit residues: 63.9806 Evaluate side-chains 234 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 809 SER Chi-restraints excluded: chain B residue 824 ARG Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 519 ILE Chi-restraints excluded: chain D residue 595 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 24 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 285 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 264 optimal weight: 0.7980 chunk 284 optimal weight: 50.0000 chunk 77 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 260 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 overall best weight: 7.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 HIS ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 960 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS A 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.075992 restraints weight = 62503.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078861 restraints weight = 39176.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079521 restraints weight = 23407.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.079946 restraints weight = 19146.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.080239 restraints weight = 18889.395| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.129 24750 Z= 0.337 Angle : 0.757 12.479 33795 Z= 0.384 Chirality : 0.045 0.215 3710 Planarity : 0.006 0.050 4257 Dihedral : 13.583 84.284 3724 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.73 % Allowed : 14.28 % Favored : 82.99 % 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: 0.78 (0.15), residues: 2872 helix: 1.35 (0.13), residues: 1514 sheet: 0.23 (0.29), residues: 297 loop : -0.54 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 466 TYR 0.026 0.002 TYR B1111 PHE 0.021 0.003 PHE B 588 TRP 0.036 0.002 TRP C 496 HIS 0.015 0.002 HIS C 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.34 (24750) covalent geometry : angle 0.75702 / 0.38 (33795) hydrogen bonds : bond 0.05057 / 3.41 ( 1195) hydrogen bonds : angle 4.45088 / 3.16 ( 3447) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 LEU cc_start: 0.8438 (tp) cc_final: 0.8166 (tt) REVERT: B 257 PHE cc_start: 0.7753 (t80) cc_final: 0.7521 (t80) REVERT: B 342 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7735 (tm-30) REVERT: B 856 CYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8265 (t) REVERT: B 1102 MET cc_start: 0.6897 (mmp) cc_final: 0.6452 (mmm) REVERT: B 1168 MET cc_start: 0.7054 (ttm) cc_final: 0.6730 (ttm) REVERT: C 1 MET cc_start: 0.8099 (tpp) cc_final: 0.7508 (tpt) REVERT: C 594 MET cc_start: 0.8934 (mmm) cc_final: 0.8676 (mmm) REVERT: C 853 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8530 (pp) REVERT: C 927 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8875 (tt) REVERT: C 981 TRP cc_start: 0.8962 (t-100) cc_final: 0.8605 (t-100) REVERT: C 1054 ASN cc_start: 0.8469 (m-40) cc_final: 0.7656 (p0) REVERT: C 1086 ASP cc_start: 0.7922 (t0) cc_final: 0.7560 (t0) REVERT: D 83 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7464 (mp0) outliers start: 67 outliers final: 46 residues processed: 249 average time/residue: 0.1393 time to fit residues: 58.3521 Evaluate side-chains 223 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 240 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 960 GLN A 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078831 restraints weight = 61729.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081546 restraints weight = 37639.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082711 restraints weight = 21522.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.082621 restraints weight = 17922.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082745 restraints weight = 17753.153| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24750 Z= 0.128 Angle : 0.586 16.424 33795 Z= 0.294 Chirality : 0.039 0.246 3710 Planarity : 0.004 0.064 4257 Dihedral : 13.455 85.928 3724 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.12 % Allowed : 15.42 % Favored : 82.46 % 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: 1.14 (0.16), residues: 2872 helix: 1.69 (0.13), residues: 1518 sheet: 0.35 (0.29), residues: 300 loop : -0.45 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 824 TYR 0.020 0.001 TYR D 404 PHE 0.015 0.001 PHE C 840 TRP 0.022 0.001 TRP C 496 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (24750) covalent geometry : angle 0.58558 / 0.29 (33795) hydrogen bonds : bond 0.03943 / 2.66 ( 1195) hydrogen bonds : angle 4.06526 / 2.88 ( 3447) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.8356 (tpp) cc_final: 0.8021 (tpp) REVERT: B 257 PHE cc_start: 0.7738 (t80) cc_final: 0.7445 (t80) REVERT: B 342 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7577 (tm-30) REVERT: B 1102 MET cc_start: 0.6730 (mmp) cc_final: 0.6357 (mmm) REVERT: B 1168 MET cc_start: 0.6953 (ttm) cc_final: 0.6746 (ttm) REVERT: C 1 MET cc_start: 0.8091 (tpp) cc_final: 0.7580 (tpt) REVERT: C 775 ARG cc_start: 0.7659 (tpp80) cc_final: 0.7046 (ttm-80) REVERT: C 853 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8376 (pp) REVERT: C 927 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8826 (tt) REVERT: C 976 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8320 (pm20) REVERT: C 1054 ASN cc_start: 0.8553 (m-40) cc_final: 0.7802 (p0) REVERT: C 1086 ASP cc_start: 0.7922 (t0) cc_final: 0.7568 (t0) REVERT: D 83 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: D 85 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.8010 (mm) outliers start: 52 outliers final: 34 residues processed: 228 average time/residue: 0.1458 time to fit residues: 56.0606 Evaluate side-chains 216 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 63 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 225 optimal weight: 0.1980 chunk 23 optimal weight: 0.0030 chunk 37 optimal weight: 0.8980 chunk 206 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 overall best weight: 1.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN D 469 HIS D 471 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.100905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080052 restraints weight = 61356.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.082431 restraints weight = 34912.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.083122 restraints weight = 22155.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083397 restraints weight = 18127.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083589 restraints weight = 16990.696| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24750 Z= 0.118 Angle : 0.576 15.128 33795 Z= 0.289 Chirality : 0.038 0.202 3710 Planarity : 0.004 0.048 4257 Dihedral : 13.382 87.004 3724 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.67 % Allowed : 16.08 % Favored : 82.25 % 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: 1.26 (0.16), residues: 2872 helix: 1.79 (0.14), residues: 1521 sheet: 0.40 (0.30), residues: 289 loop : -0.40 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 12 TYR 0.021 0.001 TYR A 62 PHE 0.014 0.001 PHE C 840 TRP 0.025 0.001 TRP C 496 HIS 0.006 0.001 HIS D 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (24750) covalent geometry : angle 0.57645 / 0.29 (33795) hydrogen bonds : bond 0.03701 / 2.50 ( 1195) hydrogen bonds : angle 3.99167 / 2.83 ( 3447) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5744 Ramachandran restraints generated. 2872 Oldfield, 0 Emsley, 2872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 136 MET cc_start: 0.8368 (tpp) cc_final: 0.8044 (tpp) REVERT: B 257 PHE cc_start: 0.7709 (t80) cc_final: 0.7408 (t80) REVERT: B 342 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7564 (tm-30) REVERT: B 453 MET cc_start: 0.7765 (mmm) cc_final: 0.7291 (tpt) REVERT: B 961 ASP cc_start: 0.8488 (t70) cc_final: 0.7886 (p0) REVERT: B 1102 MET cc_start: 0.6752 (mmp) cc_final: 0.6390 (mmm) REVERT: C 1 MET cc_start: 0.8006 (tpp) cc_final: 0.7428 (tpt) REVERT: C 775 ARG cc_start: 0.7664 (tpp80) cc_final: 0.7062 (ttm-80) REVERT: C 853 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8374 (pp) REVERT: C 927 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8791 (tt) REVERT: C 976 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: C 1031 MET cc_start: 0.8481 (mmp) cc_final: 0.8036 (tpp) REVERT: C 1054 ASN cc_start: 0.8467 (m-40) cc_final: 0.7720 (p0) REVERT: C 1086 ASP cc_start: 0.7909 (t0) cc_final: 0.7572 (t0) REVERT: D 83 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: A 23 LEU cc_start: 0.8679 (mt) cc_final: 0.8353 (mt) outliers start: 41 outliers final: 31 residues processed: 222 average time/residue: 0.1465 time to fit residues: 54.3963 Evaluate side-chains 215 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 802 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1144 ARG Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 976 GLN Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 211 optimal weight: 0.9980 chunk 285 optimal weight: 50.0000 chunk 186 optimal weight: 0.4980 chunk 88 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.080371 restraints weight = 62407.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082571 restraints weight = 38781.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083430 restraints weight = 25114.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084057 restraints weight = 19556.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084265 restraints weight = 18608.364| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24750 Z= 0.119 Angle : 0.564 15.821 33795 Z= 0.281 Chirality : 0.038 0.237 3710 Planarity : 0.004 0.049 4257 Dihedral : 13.324 86.956 3724 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.67 % Allowed : 16.16 % Favored : 82.17 % 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: 1.32 (0.16), residues: 2872 helix: 1.84 (0.14), residues: 1518 sheet: 0.39 (0.30), residues: 291 loop : -0.35 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1028 TYR 0.020 0.001 TYR D 404 PHE 0.012 0.001 PHE C 840 TRP 0.034 0.001 TRP C 496 HIS 0.004 0.001 HIS C 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (24750) covalent geometry : angle 0.56418 / 0.28 (33795) hydrogen bonds : bond 0.03625 / 2.44 ( 1195) hydrogen bonds : angle 3.95612 / 2.81 ( 3447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3198.44 seconds wall clock time: 56 minutes 21.21 seconds (3381.21 seconds total)