Starting phenix.real_space_refine on Sat Sep 12 17:37:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mr4_23956/09_2026/7mr4_23956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mr4_23956/09_2026/7mr4_23956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mr4_23956/09_2026/7mr4_23956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mr4_23956/09_2026/7mr4_23956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mr4_23956/09_2026/7mr4_23956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mr4_23956/09_2026/7mr4_23956.map" } resolution = 4.5 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: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 79 5.16 5 C 10785 2.51 5 N 3022 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17203 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 6802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6802 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 34, 'TRANS': 816} Chain breaks: 1 Chain: "C" Number of atoms: 8768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8768 Classifications: {'peptide': 1083} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1019} Chain breaks: 1 Chain: "D" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "X" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 327 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 3.46, per 1000 atoms: 0.20 Number of scatterers: 17203 At special positions: 0 Unit cell: (125.4, 103.4, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 33 15.00 O 3284 8.00 N 3022 7.00 C 10785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 758.2 milliseconds 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3906 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 16 sheets defined 59.0% alpha, 6.3% beta 9 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.518A pdb=" N ALA B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.824A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 155 through 173 removed outlier: 4.241A pdb=" N LEU B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 189 through 202 removed outlier: 5.835A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 240 removed outlier: 4.001A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 4.019A pdb=" N ARG B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.821A pdb=" N GLN B 281 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.655A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.311A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.781A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.593A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 4.089A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.664A pdb=" N GLN B 485 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 535 Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.687A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.571A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 590 " --> pdb=" O VAL B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 591 through 605 Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 624 through 632 Processing helix chain 'B' and resid 634 through 656 Processing helix chain 'B' and resid 657 through 669 removed outlier: 3.767A pdb=" N LEU B 661 " --> pdb=" O VAL B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 4.071A pdb=" N LEU B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 701 removed outlier: 4.130A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 3.590A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 808 Processing helix chain 'B' and resid 832 through 835 removed outlier: 4.200A pdb=" N GLN B 835 " --> pdb=" O ASP B 832 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 4.056A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.026A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 89 through 103 Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 4.273A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.736A 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: 4.847A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.622A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.750A pdb=" N GLU C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.752A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 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 418 through 429 Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 460 through 463 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 486 through 500 removed outlier: 4.147A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 513 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: 3.677A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 599 Proline residue: C 589 - end of helix removed outlier: 5.095A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 627 Processing helix chain 'C' and resid 633 through 647 removed outlier: 3.985A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 647 " --> pdb=" O GLN C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 723 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 834 through 843 removed outlier: 3.565A pdb=" N ALA C 842 " --> pdb=" O GLN C 838 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 852 removed outlier: 3.612A pdb=" N MET C 851 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 852 " --> pdb=" O PHE C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 890 removed outlier: 4.052A pdb=" N TYR C 878 " --> pdb=" O GLY C 874 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 887 " --> pdb=" O GLN C 883 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 888 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 910 through 934 removed outlier: 3.941A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 removed outlier: 3.644A pdb=" N VAL C 986 " --> pdb=" O LEU C 982 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.586A pdb=" N GLN C1022 " --> pdb=" O HIS C1018 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1049 removed outlier: 3.528A pdb=" N GLY C1043 " --> pdb=" O PRO C1039 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C1049 " --> pdb=" O TRP C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1076 Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 3.953A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 removed outlier: 3.555A pdb=" N ARG C1111 " --> pdb=" O GLU C1107 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C1112 " --> pdb=" O GLN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.789A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 54 through 61 removed outlier: 3.937A pdb=" N LEU D 58 " --> pdb=" O PRO D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.846A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 124 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.972A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.668A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.417A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 490 removed outlier: 3.511A pdb=" N MET B 541 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B 547 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 502 Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 558 removed outlier: 6.325A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 751 through 754 removed outlier: 3.750A pdb=" N VAL B 752 " --> pdb=" O HIS B 812 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B 814 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 754 " --> pdb=" O SER B 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.389A pdb=" N GLU C 33 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS C 214 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 211 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS C 237 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 264 through 265 removed outlier: 3.673A pdb=" N GLN C 264 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.558A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.520A pdb=" N CYS C 662 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS C 782 " --> pdb=" O PHE C 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.638A pdb=" N SER C 735 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 740 " --> pdb=" O SER C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 831 through 833 removed outlier: 6.271A pdb=" N VAL C 832 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N TRP C 955 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 965 through 967 removed outlier: 6.669A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1050 through 1051 Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 92 818 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 2.34 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: 5698 1.34 - 1.46: 3997 1.46 - 1.58: 7757 1.58 - 1.70: 64 1.70 - 1.82: 130 Bond restraints: 17646 Sorted by residual: bond pdb=" C1' DG X 12 " pdb=" N9 DG X 12 " ideal model delta sigma weight residual 1.468 1.388 0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" C1' DT X 25 " pdb=" N1 DT X 25 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.18e+01 bond pdb=" C1' DT A 64 " pdb=" N1 DT A 64 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.09e+01 bond pdb=" C1' DA X 19 " pdb=" N9 DA X 19 " ideal model delta sigma weight residual 1.468 1.391 0.077 1.40e-02 5.10e+03 3.06e+01 bond pdb=" C1' DA X 16 " pdb=" N9 DA X 16 " ideal model delta sigma weight residual 1.468 1.391 0.077 1.40e-02 5.10e+03 3.06e+01 ... (remaining 17641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 23439 2.32 - 4.65: 527 4.65 - 6.97: 96 6.97 - 9.30: 15 9.30 - 11.62: 7 Bond angle restraints: 24084 Sorted by residual: angle pdb=" C PRO B 305 " pdb=" N ARG B 306 " pdb=" CA ARG B 306 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C SER B 449 " pdb=" N ALA B 450 " pdb=" CA ALA B 450 " ideal model delta sigma weight residual 120.68 128.80 -8.12 1.52e+00 4.33e-01 2.86e+01 angle pdb=" N GLU B 696 " pdb=" CA GLU B 696 " pdb=" CB GLU B 696 " ideal model delta sigma weight residual 110.41 118.05 -7.64 1.68e+00 3.54e-01 2.07e+01 angle pdb=" CA MET C 396 " pdb=" CB MET C 396 " pdb=" CG MET C 396 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+01 angle pdb=" C GLU C 273 " pdb=" N LEU C 274 " pdb=" CA LEU C 274 " ideal model delta sigma weight residual 120.39 126.17 -5.78 1.39e+00 5.18e-01 1.73e+01 ... (remaining 24079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.62: 9907 27.62 - 55.24: 585 55.24 - 82.86: 87 82.86 - 110.49: 11 110.49 - 138.11: 1 Dihedral angle restraints: 10591 sinusoidal: 4583 harmonic: 6008 Sorted by residual: dihedral pdb=" CA PRO B 405 " pdb=" C PRO B 405 " pdb=" N GLU B 406 " pdb=" CA GLU B 406 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PRO B 755 " pdb=" C PRO B 755 " pdb=" N PHE B 756 " pdb=" CA PHE B 756 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA SER C 268 " pdb=" C SER C 268 " pdb=" N PHE C 269 " pdb=" CA PHE C 269 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 10588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1904 0.047 - 0.094: 542 0.094 - 0.141: 175 0.141 - 0.188: 21 0.188 - 0.235: 4 Chirality restraints: 2646 Sorted by residual: chirality pdb=" CB THR B 304 " pdb=" CA THR B 304 " pdb=" OG1 THR B 304 " pdb=" CG2 THR B 304 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR B 445 " pdb=" CA THR B 445 " pdb=" OG1 THR B 445 " pdb=" CG2 THR B 445 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE C 506 " pdb=" CA ILE C 506 " pdb=" CG1 ILE C 506 " pdb=" CG2 ILE C 506 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2643 not shown) Planarity restraints: 3048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 598 " 0.024 2.00e-02 2.50e+03 3.10e-02 2.40e+01 pdb=" CG TRP B 598 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP B 598 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP B 598 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 598 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 598 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 598 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 598 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 598 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 598 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO C 658 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 96 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO D 97 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 97 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 97 " 0.037 5.00e-02 4.00e+02 ... (remaining 3045 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 151 2.59 - 3.17: 13741 3.17 - 3.75: 28243 3.75 - 4.32: 35325 4.32 - 4.90: 56853 Nonbonded interactions: 134313 Sorted by model distance: nonbonded pdb=" O6 DG X 11 " pdb=" O6 DG X 12 " model vdw 2.014 3.040 nonbonded pdb=" N1 DG X 11 " pdb=" N1 DG X 12 " model vdw 2.126 3.200 nonbonded pdb=" O TRP C 496 " pdb=" OG SER C 500 " model vdw 2.222 3.040 nonbonded pdb=" C2 DA X 16 " pdb=" N2 DG A 65 " model vdw 2.236 3.420 nonbonded pdb=" OE1 GLU C 499 " pdb=" OH TYR C 550 " model vdw 2.280 3.040 ... (remaining 134308 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: 0.950 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.420 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.004 0.080 17646 Z= 0.287 Angle : 0.869 11.623 24084 Z= 0.493 Chirality : 0.049 0.235 2646 Planarity : 0.006 0.081 3048 Dihedral : 17.064 138.107 6685 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.17), residues: 2047 helix: -0.34 (0.15), residues: 1086 sheet: -1.23 (0.43), residues: 143 loop : -2.16 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 346 TYR 0.027 0.002 TYR C 714 PHE 0.032 0.002 PHE B 378 TRP 0.083 0.002 TRP B 598 HIS 0.011 0.001 HIS C 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.29 (17646) covalent geometry : angle 0.86946 / 0.49 (24084) hydrogen bonds : bond 0.15490 / 10.41 ( 839) hydrogen bonds : angle 5.96376 / 4.22 ( 2454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8264 (tmm) cc_final: 0.7663 (tmm) REVERT: B 185 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 354 MET cc_start: 0.8881 (pmm) cc_final: 0.8362 (pmm) REVERT: B 390 ASP cc_start: 0.8932 (t70) cc_final: 0.8695 (t70) REVERT: B 453 MET cc_start: 0.8799 (mmm) cc_final: 0.8352 (mmm) REVERT: B 469 MET cc_start: 0.8160 (mtp) cc_final: 0.7703 (mpp) REVERT: B 501 MET cc_start: 0.6550 (mpp) cc_final: 0.6059 (mpp) REVERT: B 616 LEU cc_start: 0.9319 (mt) cc_final: 0.9114 (mt) REVERT: B 652 TRP cc_start: 0.7349 (t60) cc_final: 0.6817 (t60) REVERT: B 849 ASP cc_start: 0.8723 (p0) cc_final: 0.8499 (p0) REVERT: C 508 ASP cc_start: 0.7917 (p0) cc_final: 0.7529 (p0) REVERT: C 568 LEU cc_start: 0.9037 (mp) cc_final: 0.8655 (tt) REVERT: C 600 LEU cc_start: 0.7334 (tp) cc_final: 0.7122 (tp) REVERT: C 609 MET cc_start: 0.9026 (mmm) cc_final: 0.8296 (mmm) REVERT: C 678 LEU cc_start: 0.9299 (mt) cc_final: 0.8852 (mt) REVERT: C 738 ASP cc_start: 0.8714 (p0) cc_final: 0.8449 (p0) REVERT: D 5 LYS cc_start: 0.6292 (pptt) cc_final: 0.6066 (pptt) REVERT: D 121 ARG cc_start: 0.7467 (mmp-170) cc_final: 0.6420 (tpm170) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1177 time to fit residues: 33.6327 Evaluate side-chains 118 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.0370 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 617 GLN C 681 ASN ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.062650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.052080 restraints weight = 96588.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.053375 restraints weight = 62985.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054310 restraints weight = 46043.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.054932 restraints weight = 36458.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.055415 restraints weight = 30760.362| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 17646 Z= 0.250 Angle : 0.691 9.164 24084 Z= 0.361 Chirality : 0.043 0.224 2646 Planarity : 0.006 0.072 3048 Dihedral : 13.948 137.952 2617 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.18), residues: 2047 helix: 0.43 (0.15), residues: 1109 sheet: -1.21 (0.41), residues: 158 loop : -2.13 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 471 TYR 0.016 0.002 TYR C1027 PHE 0.028 0.002 PHE B 756 TRP 0.035 0.002 TRP B 598 HIS 0.007 0.002 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (17646) covalent geometry : angle 0.69141 / 0.36 (24084) hydrogen bonds : bond 0.05218 / 3.47 ( 839) hydrogen bonds : angle 4.85539 / 3.44 ( 2454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.635 Fit side-chains REVERT: B 146 MET cc_start: 0.8057 (tmm) cc_final: 0.7824 (tmm) REVERT: B 200 TYR cc_start: 0.8277 (m-80) cc_final: 0.7709 (m-80) REVERT: B 354 MET cc_start: 0.8696 (pmm) cc_final: 0.8017 (pmm) REVERT: B 501 MET cc_start: 0.6918 (mpp) cc_final: 0.5900 (mpp) REVERT: B 778 LEU cc_start: 0.8962 (tt) cc_final: 0.8064 (tt) REVERT: B 849 ASP cc_start: 0.8662 (p0) cc_final: 0.8280 (p0) REVERT: C 396 MET cc_start: 0.8355 (pmm) cc_final: 0.8019 (pmm) REVERT: C 508 ASP cc_start: 0.7506 (p0) cc_final: 0.7124 (p0) REVERT: C 678 LEU cc_start: 0.9034 (mt) cc_final: 0.8646 (mm) REVERT: C 738 ASP cc_start: 0.8478 (p0) cc_final: 0.8275 (p0) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0983 time to fit residues: 23.4097 Evaluate side-chains 102 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 206 optimal weight: 30.0000 chunk 50 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 402 HIS B 650 GLN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN C 850 GLN D 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052415 restraints weight = 96024.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053737 restraints weight = 62269.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.054690 restraints weight = 45262.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.055350 restraints weight = 35710.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055842 restraints weight = 29908.461| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17646 Z= 0.163 Angle : 0.594 9.900 24084 Z= 0.311 Chirality : 0.042 0.205 2646 Planarity : 0.005 0.073 3048 Dihedral : 13.975 133.078 2617 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 2047 helix: 0.65 (0.16), residues: 1113 sheet: -1.11 (0.42), residues: 158 loop : -2.07 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 135 TYR 0.016 0.001 TYR B 514 PHE 0.015 0.001 PHE B 645 TRP 0.016 0.001 TRP B 598 HIS 0.009 0.001 HIS B 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (17646) covalent geometry : angle 0.59449 / 0.31 (24084) hydrogen bonds : bond 0.04794 / 3.20 ( 839) hydrogen bonds : angle 4.60994 / 3.27 ( 2454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.694 Fit side-chains REVERT: B 146 MET cc_start: 0.8125 (tmm) cc_final: 0.7790 (tmm) REVERT: B 200 TYR cc_start: 0.8367 (m-80) cc_final: 0.7738 (m-80) REVERT: B 354 MET cc_start: 0.8803 (pmm) cc_final: 0.8477 (ptp) REVERT: B 453 MET cc_start: 0.8890 (mmm) cc_final: 0.8667 (mmm) REVERT: B 501 MET cc_start: 0.7104 (mpp) cc_final: 0.6758 (mpp) REVERT: B 738 ILE cc_start: 0.9497 (mp) cc_final: 0.9226 (tt) REVERT: B 778 LEU cc_start: 0.8980 (tt) cc_final: 0.7774 (tt) REVERT: B 849 ASP cc_start: 0.8651 (p0) cc_final: 0.8355 (p0) REVERT: C 42 MET cc_start: 0.9455 (mmt) cc_final: 0.9235 (mmp) REVERT: C 396 MET cc_start: 0.8284 (pmm) cc_final: 0.7902 (pmm) REVERT: C 508 ASP cc_start: 0.7347 (p0) cc_final: 0.6990 (p0) REVERT: C 678 LEU cc_start: 0.9025 (mt) cc_final: 0.8614 (mm) REVERT: C 738 ASP cc_start: 0.8239 (p0) cc_final: 0.7870 (p0) REVERT: C 978 MET cc_start: 0.9279 (ppp) cc_final: 0.9028 (ppp) REVERT: D 96 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8159 (pt0) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1057 time to fit residues: 26.0826 Evaluate side-chains 105 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 126 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 179 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN C 380 HIS C 446 GLN C 522 HIS ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.061464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051107 restraints weight = 97607.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.052415 restraints weight = 63235.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.053335 restraints weight = 45924.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.053952 restraints weight = 36208.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.054434 restraints weight = 30456.011| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 17646 Z= 0.228 Angle : 0.666 11.512 24084 Z= 0.345 Chirality : 0.043 0.240 2646 Planarity : 0.005 0.070 3048 Dihedral : 14.008 131.179 2617 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 2047 helix: 0.59 (0.16), residues: 1114 sheet: -1.25 (0.42), residues: 158 loop : -2.07 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 135 TYR 0.021 0.002 TYR B 514 PHE 0.017 0.002 PHE B 645 TRP 0.021 0.002 TRP B 187 HIS 0.008 0.002 HIS B 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (17646) covalent geometry : angle 0.66649 / 0.34 (24084) hydrogen bonds : bond 0.04769 / 3.19 ( 839) hydrogen bonds : angle 4.71670 / 3.33 ( 2454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: B 146 MET cc_start: 0.8234 (tmm) cc_final: 0.8019 (tmm) REVERT: B 200 TYR cc_start: 0.8571 (m-80) cc_final: 0.8223 (m-80) REVERT: B 354 MET cc_start: 0.8709 (pmm) cc_final: 0.8142 (pmm) REVERT: B 453 MET cc_start: 0.8991 (mmm) cc_final: 0.8717 (mmm) REVERT: B 501 MET cc_start: 0.7188 (mpp) cc_final: 0.6417 (mpp) REVERT: B 738 ILE cc_start: 0.9495 (mp) cc_final: 0.9295 (tt) REVERT: B 778 LEU cc_start: 0.8964 (tt) cc_final: 0.8042 (tt) REVERT: B 849 ASP cc_start: 0.8630 (p0) cc_final: 0.8344 (p0) REVERT: C 240 PHE cc_start: 0.8880 (t80) cc_final: 0.8674 (t80) REVERT: C 396 MET cc_start: 0.8338 (pmm) cc_final: 0.7987 (pmm) REVERT: C 508 ASP cc_start: 0.7660 (p0) cc_final: 0.7346 (p0) REVERT: C 516 LEU cc_start: 0.9163 (mt) cc_final: 0.8945 (mp) REVERT: C 594 MET cc_start: 0.8504 (tpp) cc_final: 0.8064 (tpp) REVERT: C 678 LEU cc_start: 0.8954 (mt) cc_final: 0.8550 (mm) REVERT: C 697 MET cc_start: 0.8423 (mmm) cc_final: 0.8214 (mmm) REVERT: C 738 ASP cc_start: 0.8168 (p0) cc_final: 0.7861 (p0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1083 time to fit residues: 25.8830 Evaluate side-chains 104 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 61 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 281 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN D 65 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.061708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051211 restraints weight = 96650.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.052528 restraints weight = 62932.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.053458 restraints weight = 45857.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.054129 restraints weight = 36193.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.054566 restraints weight = 30227.439| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17646 Z= 0.196 Angle : 0.631 11.780 24084 Z= 0.328 Chirality : 0.042 0.240 2646 Planarity : 0.005 0.073 3048 Dihedral : 13.981 129.986 2617 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2047 helix: 0.68 (0.16), residues: 1107 sheet: -1.19 (0.43), residues: 158 loop : -1.97 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 306 TYR 0.015 0.002 TYR B 514 PHE 0.012 0.001 PHE C 465 TRP 0.050 0.002 TRP B 598 HIS 0.008 0.001 HIS B 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (17646) covalent geometry : angle 0.63127 / 0.33 (24084) hydrogen bonds : bond 0.04645 / 3.09 ( 839) hydrogen bonds : angle 4.65125 / 3.28 ( 2454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: B 146 MET cc_start: 0.8283 (tmm) cc_final: 0.7995 (tmm) REVERT: B 200 TYR cc_start: 0.8552 (m-80) cc_final: 0.8234 (m-80) REVERT: B 354 MET cc_start: 0.8691 (pmm) cc_final: 0.8106 (pmm) REVERT: B 453 MET cc_start: 0.9020 (mmm) cc_final: 0.8730 (mmm) REVERT: B 501 MET cc_start: 0.7115 (mpp) cc_final: 0.6880 (mpp) REVERT: B 778 LEU cc_start: 0.9066 (tt) cc_final: 0.8579 (tt) REVERT: B 849 ASP cc_start: 0.8490 (p0) cc_final: 0.8197 (p0) REVERT: C 240 PHE cc_start: 0.8890 (t80) cc_final: 0.8642 (t80) REVERT: C 396 MET cc_start: 0.8424 (pmm) cc_final: 0.8150 (pmm) REVERT: C 508 ASP cc_start: 0.7772 (p0) cc_final: 0.7414 (p0) REVERT: C 516 LEU cc_start: 0.9180 (mt) cc_final: 0.8831 (mm) REVERT: C 697 MET cc_start: 0.8437 (mmm) cc_final: 0.8205 (mmt) REVERT: C 738 ASP cc_start: 0.8187 (p0) cc_final: 0.7847 (p0) REVERT: C 978 MET cc_start: 0.9250 (ppp) cc_final: 0.9016 (ppp) REVERT: D 5 LYS cc_start: 0.6447 (pptt) cc_final: 0.6177 (pptt) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.1170 time to fit residues: 28.7686 Evaluate side-chains 102 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 66 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 181 GLN B 262 GLN B 281 GLN C 44 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.062248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.051639 restraints weight = 94012.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.053008 restraints weight = 60356.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053968 restraints weight = 43469.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054647 restraints weight = 34054.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.055101 restraints weight = 28390.605| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17646 Z= 0.129 Angle : 0.590 10.670 24084 Z= 0.304 Chirality : 0.041 0.227 2646 Planarity : 0.005 0.071 3048 Dihedral : 13.938 129.850 2617 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 2047 helix: 0.87 (0.16), residues: 1100 sheet: -0.99 (0.43), residues: 158 loop : -1.85 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 482 TYR 0.024 0.001 TYR B 514 PHE 0.017 0.001 PHE B 756 TRP 0.032 0.001 TRP B 598 HIS 0.007 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (17646) covalent geometry : angle 0.59021 / 0.30 (24084) hydrogen bonds : bond 0.04316 / 2.89 ( 839) hydrogen bonds : angle 4.47978 / 3.15 ( 2454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8259 (tmm) cc_final: 0.7940 (tmm) REVERT: B 200 TYR cc_start: 0.8463 (m-80) cc_final: 0.8207 (m-80) REVERT: B 354 MET cc_start: 0.8638 (pmm) cc_final: 0.7950 (pmm) REVERT: B 453 MET cc_start: 0.9025 (mmm) cc_final: 0.8737 (mmm) REVERT: B 501 MET cc_start: 0.6996 (mpp) cc_final: 0.6370 (mpp) REVERT: B 778 LEU cc_start: 0.9049 (tt) cc_final: 0.8455 (tt) REVERT: B 841 LEU cc_start: 0.9204 (mt) cc_final: 0.8686 (tt) REVERT: B 849 ASP cc_start: 0.8600 (p0) cc_final: 0.8261 (p0) REVERT: C 508 ASP cc_start: 0.7666 (p0) cc_final: 0.7303 (p0) REVERT: C 738 ASP cc_start: 0.8149 (p0) cc_final: 0.7781 (p0) REVERT: C 978 MET cc_start: 0.9169 (ppp) cc_final: 0.8958 (ppp) REVERT: D 5 LYS cc_start: 0.6440 (pptt) cc_final: 0.6151 (pptt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1122 time to fit residues: 27.8771 Evaluate side-chains 105 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 137 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 GLN B 281 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN D 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.060793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.050504 restraints weight = 97367.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.051766 restraints weight = 63553.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.052672 restraints weight = 46446.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053268 restraints weight = 36716.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.053740 restraints weight = 31007.165| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 17646 Z= 0.223 Angle : 0.676 12.346 24084 Z= 0.346 Chirality : 0.043 0.226 2646 Planarity : 0.005 0.066 3048 Dihedral : 13.965 128.292 2617 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 2047 helix: 0.76 (0.16), residues: 1102 sheet: -1.18 (0.43), residues: 159 loop : -1.93 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 306 TYR 0.015 0.002 TYR B 514 PHE 0.021 0.002 PHE B 756 TRP 0.025 0.002 TRP B 187 HIS 0.008 0.002 HIS B 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 (17646) covalent geometry : angle 0.67560 / 0.35 (24084) hydrogen bonds : bond 0.04559 / 3.06 ( 839) hydrogen bonds : angle 4.68766 / 3.30 ( 2454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: B 146 MET cc_start: 0.8296 (tmm) cc_final: 0.7957 (tmm) REVERT: B 354 MET cc_start: 0.8612 (pmm) cc_final: 0.7995 (pmm) REVERT: B 453 MET cc_start: 0.9021 (mmm) cc_final: 0.8715 (mmm) REVERT: B 778 LEU cc_start: 0.8931 (tt) cc_final: 0.8155 (tt) REVERT: B 841 LEU cc_start: 0.9189 (mt) cc_final: 0.8715 (tt) REVERT: B 849 ASP cc_start: 0.8494 (p0) cc_final: 0.8138 (p0) REVERT: C 240 PHE cc_start: 0.8850 (t80) cc_final: 0.8592 (t80) REVERT: C 508 ASP cc_start: 0.7716 (p0) cc_final: 0.7357 (p0) REVERT: C 678 LEU cc_start: 0.8914 (mm) cc_final: 0.8479 (mm) REVERT: C 738 ASP cc_start: 0.8096 (p0) cc_final: 0.7790 (p0) REVERT: C 941 MET cc_start: 0.7934 (ptt) cc_final: 0.7573 (ptt) REVERT: D 5 LYS cc_start: 0.6456 (pptt) cc_final: 0.6224 (pptt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1091 time to fit residues: 26.1446 Evaluate side-chains 103 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 150 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN D 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.062346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.051964 restraints weight = 94812.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.053283 restraints weight = 61722.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.054214 restraints weight = 44867.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054873 restraints weight = 35414.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.055316 restraints weight = 29599.850| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17646 Z= 0.128 Angle : 0.613 11.215 24084 Z= 0.314 Chirality : 0.042 0.202 2646 Planarity : 0.005 0.074 3048 Dihedral : 13.940 129.048 2617 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.19), residues: 2047 helix: 0.83 (0.16), residues: 1108 sheet: -1.04 (0.43), residues: 158 loop : -1.83 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 491 TYR 0.031 0.002 TYR B 280 PHE 0.018 0.001 PHE B 756 TRP 0.030 0.001 TRP B 598 HIS 0.007 0.001 HIS B 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (17646) covalent geometry : angle 0.61263 / 0.31 (24084) hydrogen bonds : bond 0.04201 / 2.81 ( 839) hydrogen bonds : angle 4.45748 / 3.12 ( 2454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8269 (tmm) cc_final: 0.8002 (tmm) REVERT: B 200 TYR cc_start: 0.8007 (m-80) cc_final: 0.7631 (m-80) REVERT: B 453 MET cc_start: 0.9021 (mmm) cc_final: 0.8705 (mmm) REVERT: B 501 MET cc_start: 0.7274 (mpp) cc_final: 0.6787 (mpp) REVERT: B 815 LEU cc_start: 0.9477 (pp) cc_final: 0.9250 (pp) REVERT: B 841 LEU cc_start: 0.9190 (mt) cc_final: 0.8750 (tt) REVERT: B 849 ASP cc_start: 0.8597 (p0) cc_final: 0.8263 (p0) REVERT: C 240 PHE cc_start: 0.8907 (t80) cc_final: 0.8583 (t80) REVERT: C 508 ASP cc_start: 0.7634 (p0) cc_final: 0.7232 (p0) REVERT: C 738 ASP cc_start: 0.8206 (p0) cc_final: 0.7821 (p0) REVERT: D 5 LYS cc_start: 0.6448 (pptt) cc_final: 0.6219 (pptt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1126 time to fit residues: 28.4179 Evaluate side-chains 110 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 144 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 139 optimal weight: 0.5980 chunk 166 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.062216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.051792 restraints weight = 96107.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.053116 restraints weight = 61962.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.054067 restraints weight = 44943.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.054742 restraints weight = 35296.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055182 restraints weight = 29413.976| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17646 Z= 0.143 Angle : 0.611 10.786 24084 Z= 0.314 Chirality : 0.042 0.199 2646 Planarity : 0.005 0.068 3048 Dihedral : 13.917 128.055 2617 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.19), residues: 2047 helix: 0.86 (0.16), residues: 1112 sheet: -1.02 (0.43), residues: 158 loop : -1.82 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 491 TYR 0.017 0.001 TYR B 514 PHE 0.015 0.001 PHE B 756 TRP 0.026 0.001 TRP B 187 HIS 0.007 0.001 HIS B 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (17646) covalent geometry : angle 0.61096 / 0.31 (24084) hydrogen bonds : bond 0.04114 / 2.75 ( 839) hydrogen bonds : angle 4.47437 / 3.12 ( 2454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8285 (tmm) cc_final: 0.8007 (tmm) REVERT: B 200 TYR cc_start: 0.8102 (m-80) cc_final: 0.7881 (m-80) REVERT: B 453 MET cc_start: 0.9016 (mmm) cc_final: 0.8712 (mmm) REVERT: B 501 MET cc_start: 0.7245 (mpp) cc_final: 0.6792 (mpp) REVERT: B 815 LEU cc_start: 0.9488 (pp) cc_final: 0.9265 (pp) REVERT: B 841 LEU cc_start: 0.9186 (mt) cc_final: 0.8761 (tt) REVERT: B 849 ASP cc_start: 0.8590 (p0) cc_final: 0.8258 (p0) REVERT: C 240 PHE cc_start: 0.8911 (t80) cc_final: 0.8595 (t80) REVERT: C 508 ASP cc_start: 0.7607 (p0) cc_final: 0.7215 (p0) REVERT: C 738 ASP cc_start: 0.8210 (p0) cc_final: 0.7826 (p0) REVERT: C 941 MET cc_start: 0.7899 (ptt) cc_final: 0.7626 (ptt) REVERT: D 5 LYS cc_start: 0.6467 (pptt) cc_final: 0.6214 (pptt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1007 time to fit residues: 25.8400 Evaluate side-chains 108 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 163 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 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 = 0.3241 r_free = 0.3241 target = 0.062609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.052144 restraints weight = 94826.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.053487 restraints weight = 61275.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.054439 restraints weight = 44340.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.055097 restraints weight = 34820.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.055603 restraints weight = 29070.786| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17646 Z= 0.124 Angle : 0.605 9.892 24084 Z= 0.310 Chirality : 0.041 0.184 2646 Planarity : 0.004 0.072 3048 Dihedral : 13.884 127.960 2617 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 2047 helix: 0.88 (0.16), residues: 1112 sheet: -1.08 (0.45), residues: 148 loop : -1.78 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 491 TYR 0.020 0.001 TYR B 280 PHE 0.013 0.001 PHE C 901 TRP 0.029 0.001 TRP B 187 HIS 0.006 0.001 HIS B 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (17646) covalent geometry : angle 0.60534 / 0.31 (24084) hydrogen bonds : bond 0.04003 / 2.67 ( 839) hydrogen bonds : angle 4.42404 / 3.08 ( 2454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8225 (tmm) cc_final: 0.7957 (tmm) REVERT: B 453 MET cc_start: 0.9004 (mmm) cc_final: 0.8698 (mmm) REVERT: B 501 MET cc_start: 0.7115 (mpp) cc_final: 0.6851 (mpp) REVERT: B 841 LEU cc_start: 0.9156 (mt) cc_final: 0.8705 (tt) REVERT: B 849 ASP cc_start: 0.8568 (p0) cc_final: 0.8275 (p0) REVERT: C 240 PHE cc_start: 0.8845 (t80) cc_final: 0.8579 (t80) REVERT: C 508 ASP cc_start: 0.7595 (p0) cc_final: 0.7209 (p0) REVERT: C 738 ASP cc_start: 0.8197 (p0) cc_final: 0.7817 (p0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1056 time to fit residues: 26.8011 Evaluate side-chains 106 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 185 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 125 optimal weight: 0.0970 chunk 91 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1022 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.062043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.051627 restraints weight = 95847.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052909 restraints weight = 62090.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053868 restraints weight = 45444.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054492 restraints weight = 35759.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.055006 restraints weight = 29980.071| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17646 Z= 0.159 Angle : 0.624 10.861 24084 Z= 0.319 Chirality : 0.042 0.189 2646 Planarity : 0.004 0.068 3048 Dihedral : 13.882 127.225 2617 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 2047 helix: 0.88 (0.16), residues: 1113 sheet: -1.10 (0.45), residues: 148 loop : -1.78 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 491 TYR 0.015 0.002 TYR B 394 PHE 0.014 0.001 PHE B 645 TRP 0.032 0.001 TRP B 187 HIS 0.007 0.001 HIS B 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (17646) covalent geometry : angle 0.62409 / 0.32 (24084) hydrogen bonds : bond 0.04057 / 2.71 ( 839) hydrogen bonds : angle 4.49444 / 3.13 ( 2454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2049.99 seconds wall clock time: 36 minutes 33.97 seconds (2193.97 seconds total)