Starting phenix.real_space_refine on Mon Aug 25 00:27:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b1u_15805/08_2025/8b1u_15805.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b1u_15805/08_2025/8b1u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2025/8b1u_15805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2025/8b1u_15805.map" model { file = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2025/8b1u_15805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b1u_15805/08_2025/8b1u_15805.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.00, per 1000 atoms: 0.25 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: 2.36 Conformation dependent library (CDL) restraints added in 939.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 3.20 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: 6.14 Time building geometry restraints manager: 3.05 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=" 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=" O3G ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.528 1.581 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" O2B ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.508 1.556 -0.048 2.00e-02 2.50e+03 5.74e+00 ... (remaining 24745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 33745 3.41 - 6.81: 43 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=" O1B ANP B1501 " pdb=" PB ANP B1501 " pdb=" O2B ANP B1501 " ideal model delta sigma weight residual 120.08 109.49 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA LEU C 323 " pdb=" CB LEU C 323 " pdb=" CG LEU C 323 " ideal model delta sigma weight residual 116.30 126.52 -10.22 3.50e+00 8.16e-02 8.53e+00 angle pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " pdb=" O2G ANP B1501 " ideal model delta sigma weight residual 101.05 109.44 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" C PRO B 174 " pdb=" N LEU B 175 " pdb=" CA LEU B 175 " ideal model delta sigma weight residual 120.51 124.40 -3.89 1.45e+00 4.76e-01 7.18e+00 ... (remaining 33790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 13903 17.67 - 35.35: 608 35.35 - 53.02: 227 53.02 - 70.70: 85 70.70 - 88.37: 10 Dihedral angle restraints: 14833 sinusoidal: 6431 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 14830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3253 0.052 - 0.104: 394 0.104 - 0.155: 61 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: 0.820 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.350 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.002 0.143 24750 Z= 0.136 Angle : 0.512 17.029 33795 Z= 0.307 Chirality : 0.035 0.259 3710 Planarity : 0.003 0.053 4257 Dihedral : 12.357 88.373 9387 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 aren 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 covalent geometry : bond 0.00249 (24750) covalent geometry : angle 0.51176 (33795) hydrogen bonds : bond 0.15269 ( 1195) hydrogen bonds : angle 5.47088 ( 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 : 0.990 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: 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: 0.8551 (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: 0.2104 time to fit residues: 209.2238 Evaluate side-chains 263 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 257 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 150 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 B1134 HIS B1161 ASN C 87 ASN C 137 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 HIS C 390 HIS C 448 HIS C 510 ASN C 739 ASN C 759 HIS ** C 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN D 50 HIS D 247 GLN D 256 HIS D 469 HIS D 542 GLN A 63 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080416 restraints weight = 61241.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082943 restraints weight = 36103.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083654 restraints weight = 22472.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.084230 restraints weight = 18092.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084337 restraints weight = 16880.791| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 24750 Z= 0.246 Angle : 0.682 11.081 33795 Z= 0.351 Chirality : 0.043 0.205 3710 Planarity : 0.005 0.064 4257 Dihedral : 13.711 89.221 3761 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.94 % Allowed : 10.44 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.15), residues: 2872 helix: 1.10 (0.13), residues: 1504 sheet: -0.32 (0.27), residues: 307 loop : -0.53 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 58 TYR 0.025 0.002 TYR B1111 PHE 0.023 0.002 PHE C 125 TRP 0.020 0.002 TRP C 574 HIS 0.010 0.001 HIS D 473 Details of bonding type rmsd covalent geometry : bond 0.00575 (24750) covalent geometry : angle 0.68200 (33795) hydrogen bonds : bond 0.04937 ( 1195) hydrogen bonds : angle 4.45899 ( 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 317 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 245 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7449 (tm-30) REVERT: B 518 MET cc_start: 0.8687 (mmm) cc_final: 0.8296 (mmm) REVERT: B 960 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7806 (tp30) REVERT: B 1021 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7559 (ptp) REVERT: C 712 ASP cc_start: 0.8405 (m-30) cc_final: 0.8090 (m-30) REVERT: C 981 TRP cc_start: 0.8998 (t-100) cc_final: 0.8597 (t-100) REVERT: C 1054 ASN cc_start: 0.8453 (m-40) cc_final: 0.7645 (p0) REVERT: C 1086 ASP cc_start: 0.7843 (t0) cc_final: 0.7492 (t0) REVERT: D 83 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: D 279 MET cc_start: 0.9208 (tpt) cc_final: 0.8812 (mmm) REVERT: D 314 CYS cc_start: 0.7735 (t) cc_final: 0.7425 (t) REVERT: A 9 ASP cc_start: 0.8105 (p0) cc_final: 0.7828 (p0) REVERT: A 28 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8154 (mtmm) REVERT: A 61 ILE cc_start: 0.7681 (tp) cc_final: 0.7453 (pt) outliers start: 72 outliers final: 41 residues processed: 307 average time/residue: 0.1686 time to fit residues: 83.0429 Evaluate side-chains 231 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 380 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 883 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 C residue 176 THR Chi-restraints excluded: chain C residue 251 ILE 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 752 ILE 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 160 VAL 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 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: 6.9990 chunk 245 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 224 optimal weight: 9.9990 chunk 284 optimal weight: 20.0000 chunk 189 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 278 optimal weight: 0.7980 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 HIS B 484 ASN B 705 HIS B 879 GLN B 971 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 HIS C 881 ASN D 439 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079449 restraints weight = 61129.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082277 restraints weight = 38723.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082917 restraints weight = 22131.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.083075 restraints weight = 19415.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.083081 restraints weight = 18736.960| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24750 Z= 0.191 Angle : 0.591 9.820 33795 Z= 0.304 Chirality : 0.040 0.172 3710 Planarity : 0.004 0.049 4257 Dihedral : 13.523 82.222 3755 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.98 % Allowed : 12.44 % Favored : 84.58 % 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 aren not related in a simple way. whole: 0.84 (0.15), residues: 2872 helix: 1.42 (0.13), residues: 1514 sheet: -0.01 (0.28), residues: 305 loop : -0.44 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 297 TYR 0.024 0.002 TYR B1111 PHE 0.016 0.002 PHE C 840 TRP 0.016 0.001 TRP B 652 HIS 0.008 0.001 HIS D 473 Details of bonding type rmsd covalent geometry : bond 0.00449 (24750) covalent geometry : angle 0.59145 (33795) hydrogen bonds : bond 0.04391 ( 1195) hydrogen bonds : angle 4.21734 ( 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 287 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 SER cc_start: 0.8777 (m) cc_final: 0.8529 (t) REVERT: B 65 THR cc_start: 0.8812 (m) cc_final: 0.8571 (m) REVERT: B 342 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 667 MET cc_start: 0.8492 (mmp) cc_final: 0.7924 (mmm) REVERT: C 712 ASP cc_start: 0.8308 (m-30) cc_final: 0.7999 (m-30) REVERT: C 897 LEU cc_start: 0.9183 (mt) cc_final: 0.8939 (mt) REVERT: C 927 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8861 (tt) REVERT: C 981 TRP cc_start: 0.8999 (t-100) cc_final: 0.8542 (t-100) REVERT: C 1054 ASN cc_start: 0.8481 (m-40) cc_final: 0.7839 (p0) REVERT: C 1086 ASP cc_start: 0.7907 (t0) cc_final: 0.7558 (t0) REVERT: D 83 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: D 572 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6717 (mmp-170) REVERT: A 28 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8106 (mtmm) REVERT: A 61 ILE cc_start: 0.7799 (tp) cc_final: 0.7586 (pt) outliers start: 73 outliers final: 40 residues processed: 278 average time/residue: 0.1679 time to fit residues: 74.8928 Evaluate side-chains 224 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 326 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 567 VAL 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 968 VAL Chi-restraints excluded: chain B residue 1032 ILE 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 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 612 ILE Chi-restraints excluded: chain C residue 752 ILE 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 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR 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 28 LYS 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: 10.0000 chunk 203 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 879 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 HIS D 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076302 restraints weight = 62185.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.078187 restraints weight = 36761.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079309 restraints weight = 23670.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.079563 restraints weight = 18977.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079839 restraints weight = 18654.565| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 24750 Z= 0.293 Angle : 0.686 9.498 33795 Z= 0.352 Chirality : 0.044 0.455 3710 Planarity : 0.005 0.062 4257 Dihedral : 13.720 85.118 3755 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.59 % Allowed : 13.42 % 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 aren not related in a simple way. whole: 0.64 (0.15), residues: 2872 helix: 1.22 (0.13), residues: 1516 sheet: -0.02 (0.28), residues: 298 loop : -0.52 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 57 TYR 0.026 0.002 TYR B1111 PHE 0.021 0.002 PHE B 588 TRP 0.033 0.002 TRP C 955 HIS 0.011 0.001 HIS C 784 Details of bonding type rmsd covalent geometry : bond 0.00692 (24750) covalent geometry : angle 0.68556 (33795) hydrogen bonds : bond 0.05006 ( 1195) hydrogen bonds : angle 4.52488 ( 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 287 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 199 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 LEU cc_start: 0.8421 (tp) cc_final: 0.8148 (tt) REVERT: B 342 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 856 CYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8221 (t) REVERT: B 968 VAL cc_start: 0.7116 (t) cc_final: 0.6678 (t) REVERT: B 1168 MET cc_start: 0.7082 (ttm) cc_final: 0.6755 (ttm) REVERT: C 1 MET cc_start: 0.8216 (tpp) cc_final: 0.7701 (tpt) REVERT: C 667 MET cc_start: 0.8652 (mmp) cc_final: 0.7970 (mmm) REVERT: C 786 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7313 (ttm-80) REVERT: C 853 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8523 (pp) REVERT: C 927 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8919 (tt) REVERT: C 981 TRP cc_start: 0.9008 (t-100) cc_final: 0.8647 (t-100) REVERT: C 993 ASN cc_start: 0.7218 (t0) cc_final: 0.7005 (t0) REVERT: C 1054 ASN cc_start: 0.8559 (m-40) cc_final: 0.7755 (p0) REVERT: C 1086 ASP cc_start: 0.7954 (t0) cc_final: 0.7667 (t0) REVERT: D 67 LEU cc_start: 0.7309 (tp) cc_final: 0.7098 (tp) REVERT: D 83 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: D 279 MET cc_start: 0.9307 (tpt) cc_final: 0.9001 (tpt) REVERT: A 25 LYS cc_start: 0.8873 (tppt) cc_final: 0.8629 (tptp) REVERT: A 28 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8241 (mtmm) outliers start: 88 outliers final: 55 residues processed: 274 average time/residue: 0.1589 time to fit residues: 71.6097 Evaluate side-chains 231 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 323 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 735 LEU 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 879 GLN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 941 THR 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 109 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 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 497 VAL 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 786 ARG Chi-restraints excluded: chain C residue 821 VAL 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 C residue 1116 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 352 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: 1.9990 chunk 147 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 97 optimal weight: 0.0040 chunk 50 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 594 GLN B 726 GLN B 834 HIS B 879 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 881 ASN C 960 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079076 restraints weight = 60974.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.081427 restraints weight = 38695.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082556 restraints weight = 23066.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082530 restraints weight = 19151.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082623 restraints weight = 19006.862| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4526 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= 0.124 Angle : 0.550 10.582 33795 Z= 0.280 Chirality : 0.038 0.214 3710 Planarity : 0.004 0.045 4257 Dihedral : 13.476 89.620 3755 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.73 % Allowed : 14.48 % Favored : 82.78 % 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 aren not related in a simple way. whole: 1.00 (0.16), residues: 2872 helix: 1.59 (0.13), residues: 1521 sheet: 0.18 (0.29), residues: 301 loop : -0.50 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1028 TYR 0.021 0.001 TYR B1111 PHE 0.023 0.001 PHE B 257 TRP 0.037 0.001 TRP C 955 HIS 0.004 0.001 HIS C 784 Details of bonding type rmsd covalent geometry : bond 0.00284 (24750) covalent geometry : angle 0.54953 (33795) hydrogen bonds : bond 0.03865 ( 1195) hydrogen bonds : angle 4.10104 ( 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 266 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 199 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 THR cc_start: 0.8897 (m) cc_final: 0.8622 (m) REVERT: B 342 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7539 (tm-30) REVERT: B 901 TRP cc_start: 0.8757 (OUTLIER) cc_final: 0.8337 (t60) REVERT: B 1171 MET cc_start: 0.9101 (tmm) cc_final: 0.8798 (ppp) REVERT: C 1 MET cc_start: 0.8223 (tpp) cc_final: 0.7663 (tpt) REVERT: C 667 MET cc_start: 0.8469 (mmp) cc_final: 0.8263 (mmt) REVERT: C 775 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7092 (ttm-80) REVERT: C 853 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8466 (pp) REVERT: C 927 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8834 (tt) REVERT: C 981 TRP cc_start: 0.9036 (t-100) cc_final: 0.8583 (t-100) REVERT: C 1031 MET cc_start: 0.8417 (mmp) cc_final: 0.7889 (tpp) REVERT: C 1054 ASN cc_start: 0.8461 (m-40) cc_final: 0.7774 (p0) REVERT: D 83 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: D 85 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7974 (mm) REVERT: D 279 MET cc_start: 0.9331 (tpt) cc_final: 0.8960 (tpt) REVERT: A 28 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8173 (mtmm) outliers start: 67 outliers final: 34 residues processed: 259 average time/residue: 0.1601 time to fit residues: 67.7155 Evaluate side-chains 213 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 238 ASP 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 879 GLN Chi-restraints excluded: chain B residue 901 TRP 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 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 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 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 85 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 141 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 0.0030 chunk 14 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 180 optimal weight: 0.5980 overall best weight: 3.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 879 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS A 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077538 restraints weight = 61590.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080448 restraints weight = 37972.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.081214 restraints weight = 22113.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.081418 restraints weight = 18022.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.081731 restraints weight = 18330.109| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24750 Z= 0.170 Angle : 0.571 9.809 33795 Z= 0.292 Chirality : 0.039 0.150 3710 Planarity : 0.004 0.046 4257 Dihedral : 13.455 89.139 3753 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.98 % Allowed : 14.81 % Favored : 82.21 % 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 aren not related in a simple way. whole: 1.04 (0.16), residues: 2872 helix: 1.63 (0.13), residues: 1519 sheet: 0.23 (0.29), residues: 301 loop : -0.50 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 23 TYR 0.023 0.001 TYR D 404 PHE 0.014 0.001 PHE C 125 TRP 0.035 0.001 TRP C 955 HIS 0.007 0.001 HIS C 784 Details of bonding type rmsd covalent geometry : bond 0.00402 (24750) covalent geometry : angle 0.57116 (33795) hydrogen bonds : bond 0.04054 ( 1195) hydrogen bonds : angle 4.12320 ( 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 257 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 184 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7572 (tm-30) REVERT: B 728 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7362 (mtt90) REVERT: B 901 TRP cc_start: 0.8783 (OUTLIER) cc_final: 0.8314 (t60) REVERT: B 961 ASP cc_start: 0.8577 (t70) cc_final: 0.7882 (p0) REVERT: B 1050 CYS cc_start: 0.7478 (m) cc_final: 0.7031 (m) REVERT: C 1 MET cc_start: 0.8294 (tpp) cc_final: 0.7823 (tpt) REVERT: C 667 MET cc_start: 0.8600 (mmp) cc_final: 0.8377 (mmt) REVERT: C 786 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7195 (ttm-80) REVERT: C 853 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8419 (pp) REVERT: C 927 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8847 (tt) REVERT: C 1054 ASN cc_start: 0.8438 (m-40) cc_final: 0.7692 (p0) REVERT: D 81 TRP cc_start: 0.5812 (m100) cc_final: 0.5313 (m100) REVERT: D 83 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: D 85 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8054 (mm) REVERT: D 279 MET cc_start: 0.9341 (tpt) cc_final: 0.8953 (tpt) REVERT: A 28 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8200 (mtmm) outliers start: 73 outliers final: 45 residues processed: 248 average time/residue: 0.1655 time to fit residues: 66.6660 Evaluate side-chains 229 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 238 ASP 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 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 856 CYS Chi-restraints excluded: chain B residue 879 GLN Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 901 TRP 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 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 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 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 828 LEU 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 85 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 228 optimal weight: 20.0000 chunk 39 optimal weight: 0.0570 chunk 209 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 overall best weight: 3.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 879 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077374 restraints weight = 61597.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079802 restraints weight = 37579.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080932 restraints weight = 22335.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080914 restraints weight = 18504.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081138 restraints weight = 18019.383| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24750 Z= 0.171 Angle : 0.577 11.410 33795 Z= 0.293 Chirality : 0.039 0.245 3710 Planarity : 0.004 0.046 4257 Dihedral : 13.431 89.467 3753 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.98 % Allowed : 15.46 % Favored : 81.56 % 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 aren not related in a simple way. whole: 1.04 (0.16), residues: 2872 helix: 1.62 (0.13), residues: 1523 sheet: 0.25 (0.29), residues: 300 loop : -0.51 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1028 TYR 0.029 0.002 TYR D 477 PHE 0.020 0.001 PHE C 125 TRP 0.032 0.001 TRP C 955 HIS 0.006 0.001 HIS C 784 Details of bonding type rmsd covalent geometry : bond 0.00404 (24750) covalent geometry : angle 0.57701 (33795) hydrogen bonds : bond 0.04021 ( 1195) hydrogen bonds : angle 4.11131 ( 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 252 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 179 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7625 (tm-30) REVERT: B 728 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7372 (mtt90) REVERT: B 901 TRP cc_start: 0.8791 (OUTLIER) cc_final: 0.8319 (t60) REVERT: B 961 ASP cc_start: 0.8526 (t70) cc_final: 0.7769 (p0) REVERT: B 1050 CYS cc_start: 0.7485 (m) cc_final: 0.7070 (m) REVERT: C 1 MET cc_start: 0.8284 (tpp) cc_final: 0.7972 (tpt) REVERT: C 667 MET cc_start: 0.8599 (mmp) cc_final: 0.8372 (mmt) REVERT: C 786 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7349 (ttm-80) REVERT: C 853 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8423 (pp) REVERT: C 927 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8811 (tt) REVERT: C 1054 ASN cc_start: 0.8495 (m-40) cc_final: 0.7709 (p0) REVERT: D 83 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: D 412 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8719 (tt) REVERT: D 523 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: A 28 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8307 (mtmm) outliers start: 73 outliers final: 49 residues processed: 245 average time/residue: 0.1575 time to fit residues: 62.7502 Evaluate side-chains 226 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 238 ASP 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 644 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 735 LEU 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 901 TRP Chi-restraints excluded: chain B residue 941 THR 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 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 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 528 LEU 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 786 ARG Chi-restraints excluded: chain C residue 828 LEU 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 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 523 GLN Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 285 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 264 optimal weight: 0.6980 chunk 284 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 260 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.079066 restraints weight = 61225.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.080955 restraints weight = 37506.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081884 restraints weight = 23698.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.082072 restraints weight = 21248.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.082475 restraints weight = 19823.965| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24750 Z= 0.124 Angle : 0.551 12.635 33795 Z= 0.277 Chirality : 0.038 0.186 3710 Planarity : 0.004 0.049 4257 Dihedral : 13.339 89.784 3753 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.37 % Allowed : 15.87 % Favored : 81.76 % 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 aren not related in a simple way. whole: 1.19 (0.16), residues: 2872 helix: 1.76 (0.13), residues: 1520 sheet: 0.30 (0.30), residues: 300 loop : -0.46 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 824 TYR 0.023 0.001 TYR D 404 PHE 0.020 0.001 PHE B 257 TRP 0.025 0.001 TRP C 955 HIS 0.004 0.001 HIS C 784 Details of bonding type rmsd covalent geometry : bond 0.00289 (24750) covalent geometry : angle 0.55113 (33795) hydrogen bonds : bond 0.03654 ( 1195) hydrogen bonds : angle 3.98355 ( 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 242 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: B 11 LEU cc_start: 0.8495 (tt) cc_final: 0.8282 (tp) REVERT: B 342 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 728 ARG cc_start: 0.7599 (mtt180) cc_final: 0.7351 (mtt90) REVERT: B 901 TRP cc_start: 0.8768 (OUTLIER) cc_final: 0.8336 (t60) REVERT: B 961 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7718 (p0) REVERT: C 1 MET cc_start: 0.8227 (tpp) cc_final: 0.7922 (tpt) REVERT: C 775 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7082 (ttm-80) REVERT: C 786 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7209 (ttm-80) REVERT: C 927 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8757 (tt) REVERT: C 1054 ASN cc_start: 0.8334 (m-40) cc_final: 0.7619 (p0) REVERT: D 523 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: A 28 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8157 (mtmm) outliers start: 58 outliers final: 36 residues processed: 235 average time/residue: 0.1695 time to fit residues: 64.5510 Evaluate side-chains 215 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 238 ASP 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 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain B residue 1032 ILE 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 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 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 523 GLN Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 240 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 58 optimal weight: 0.0870 chunk 56 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076667 restraints weight = 62443.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.079076 restraints weight = 38344.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.080301 restraints weight = 23115.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080388 restraints weight = 18631.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080495 restraints weight = 17855.286| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5145 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= 0.213 Angle : 0.622 13.688 33795 Z= 0.313 Chirality : 0.041 0.292 3710 Planarity : 0.004 0.045 4257 Dihedral : 13.442 89.369 3753 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.53 % Allowed : 15.83 % Favored : 81.64 % 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 aren not related in a simple way. whole: 1.00 (0.16), residues: 2872 helix: 1.61 (0.13), residues: 1523 sheet: 0.13 (0.30), residues: 287 loop : -0.52 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 824 TYR 0.025 0.002 TYR D 404 PHE 0.018 0.002 PHE C 125 TRP 0.033 0.002 TRP C 955 HIS 0.007 0.001 HIS C 784 Details of bonding type rmsd covalent geometry : bond 0.00505 (24750) covalent geometry : angle 0.62245 (33795) hydrogen bonds : bond 0.04249 ( 1195) hydrogen bonds : angle 4.18024 ( 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 247 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: B 274 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6030 (tt0) REVERT: B 342 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 728 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7390 (mtt90) REVERT: B 961 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.7779 (p0) REVERT: C 1 MET cc_start: 0.8331 (tpp) cc_final: 0.7963 (tpt) REVERT: C 786 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7328 (ttm-80) REVERT: C 927 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8869 (tt) REVERT: C 1054 ASN cc_start: 0.8444 (m-40) cc_final: 0.7622 (p0) REVERT: A 9 ASP cc_start: 0.8115 (p0) cc_final: 0.7813 (p0) REVERT: A 28 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8250 (mtmm) outliers start: 62 outliers final: 45 residues processed: 239 average time/residue: 0.1697 time to fit residues: 65.7451 Evaluate side-chains 227 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 238 ASP 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 567 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 636 HIS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET 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 961 ASP Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain B residue 1111 TYR 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 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 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 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 293 random chunks: chunk 225 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.075479 restraints weight = 62179.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.077929 restraints weight = 38289.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078982 restraints weight = 22469.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078876 restraints weight = 19057.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.079199 restraints weight = 18262.088| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 24750 Z= 0.256 Angle : 0.684 14.159 33795 Z= 0.344 Chirality : 0.042 0.218 3710 Planarity : 0.005 0.044 4257 Dihedral : 13.608 89.781 3753 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.12 % Allowed : 16.36 % Favored : 81.52 % 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 aren not related in a simple way. whole: 0.69 (0.16), residues: 2872 helix: 1.33 (0.13), residues: 1527 sheet: -0.05 (0.30), residues: 287 loop : -0.61 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 947 TYR 0.038 0.002 TYR D 477 PHE 0.017 0.002 PHE C 125 TRP 0.041 0.002 TRP B1085 HIS 0.009 0.001 HIS C 784 Details of bonding type rmsd covalent geometry : bond 0.00605 (24750) covalent geometry : angle 0.68373 (33795) hydrogen bonds : bond 0.04730 ( 1195) hydrogen bonds : angle 4.38926 ( 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 230 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 178 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: B 342 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7670 (tm-30) REVERT: B 728 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7391 (mtt90) REVERT: B 856 CYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8212 (t) REVERT: B 961 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7862 (p0) REVERT: C 1 MET cc_start: 0.8299 (tpp) cc_final: 0.7796 (tpt) REVERT: C 665 MET cc_start: 0.7561 (ptm) cc_final: 0.7359 (ptm) REVERT: C 786 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7409 (ttm-80) REVERT: C 927 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8807 (tt) REVERT: C 981 TRP cc_start: 0.9013 (t-100) cc_final: 0.8627 (t-100) REVERT: C 1054 ASN cc_start: 0.8471 (m-40) cc_final: 0.7614 (p0) REVERT: A 23 LEU cc_start: 0.8483 (mt) cc_final: 0.8258 (mt) outliers start: 52 outliers final: 36 residues processed: 222 average time/residue: 0.1636 time to fit residues: 59.1604 Evaluate side-chains 214 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 238 ASP 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 644 GLU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET 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 961 ASP Chi-restraints excluded: chain B residue 1032 ILE 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 419 SER Chi-restraints excluded: chain C residue 428 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 588 LEU Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 352 LEU 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: 1.9990 chunk 285 optimal weight: 20.0000 chunk 186 optimal weight: 0.0570 chunk 88 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.077275 restraints weight = 61566.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.079311 restraints weight = 37458.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.080777 restraints weight = 23484.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080842 restraints weight = 17848.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081137 restraints weight = 17609.874| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24750 Z= 0.156 Angle : 0.606 14.614 33795 Z= 0.301 Chirality : 0.039 0.231 3710 Planarity : 0.004 0.045 4257 Dihedral : 13.466 88.644 3753 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.84 % Allowed : 16.97 % Favored : 81.19 % 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 aren not related in a simple way. whole: 0.95 (0.16), residues: 2872 helix: 1.58 (0.13), residues: 1515 sheet: 0.06 (0.30), residues: 287 loop : -0.54 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1028 TYR 0.025 0.002 TYR D 404 PHE 0.016 0.001 PHE C 125 TRP 0.030 0.001 TRP C 955 HIS 0.005 0.001 HIS C 784 Details of bonding type rmsd covalent geometry : bond 0.00367 (24750) covalent geometry : angle 0.60554 (33795) hydrogen bonds : bond 0.03994 ( 1195) hydrogen bonds : angle 4.14444 ( 3447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3427.89 seconds wall clock time: 60 minutes 27.03 seconds (3627.03 seconds total)