Starting phenix.real_space_refine on Wed Mar 4 23:34:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mr4_23956/03_2026/7mr4_23956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mr4_23956/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mr4_23956/03_2026/7mr4_23956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mr4_23956/03_2026/7mr4_23956.map" model { file = "/net/cci-nas-00/data/ceres_data/7mr4_23956/03_2026/7mr4_23956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mr4_23956/03_2026/7mr4_23956.cif" } 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-dev-5986/lib/python3.9/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: 2.99, per 1000 atoms: 0.17 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: 1.45 Conformation dependent library (CDL) restraints added in 676.1 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: 1.86 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: 3.08 Time building geometry restraints manager: 1.93 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=" C LEU C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.83e+01 bond pdb=" C TYR B 173 " pdb=" N PRO B 174 " ideal model delta sigma weight residual 1.334 1.369 -0.035 8.40e-03 1.42e+04 1.77e+01 bond pdb=" C1' DG X 12 " pdb=" N9 DG X 12 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C1' DA X 19 " pdb=" N9 DA X 19 " ideal model delta sigma weight residual 1.460 1.391 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1' DA X 16 " pdb=" N9 DA X 16 " ideal model delta sigma weight residual 1.460 1.391 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 17641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 23422 2.32 - 4.65: 544 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: 1930 0.047 - 0.094: 531 0.094 - 0.141: 160 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 0.072 17646 Z= 0.204 Angle : 0.865 11.623 24084 Z= 0.467 Chirality : 0.048 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 covalent geometry : bond 0.00407 (17646) covalent geometry : angle 0.86473 (24084) hydrogen bonds : bond 0.15490 ( 839) hydrogen bonds : angle 5.96376 ( 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 : 0.636 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: 0.7662 (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: 0.8361 (pmm) REVERT: B 390 ASP cc_start: 0.8932 (t70) cc_final: 0.8696 (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: 0.6060 (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: 0.6816 (t60) REVERT: B 849 ASP cc_start: 0.8723 (p0) cc_final: 0.8498 (p0) REVERT: C 508 ASP cc_start: 0.7917 (p0) cc_final: 0.7531 (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: 0.7120 (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: 0.6068 (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: 0.1168 time to fit residues: 33.4047 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 : 0.655 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 402 HIS ** 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 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN ** D 32 HIS ** 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 = 0.3208 r_free = 0.3208 target = 0.061657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051079 restraints weight = 96729.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.052366 restraints weight = 63066.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.053293 restraints weight = 46185.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.053901 restraints weight = 36575.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054391 restraints weight = 30954.779| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 17646 Z= 0.253 Angle : 0.697 11.140 24084 Z= 0.362 Chirality : 0.043 0.157 2646 Planarity : 0.005 0.070 3048 Dihedral : 13.838 131.438 2617 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % 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: -0.95 (0.18), residues: 2047 helix: 0.47 (0.15), residues: 1113 sheet: -1.22 (0.41), residues: 158 loop : -2.12 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 471 TYR 0.017 0.002 TYR B 768 PHE 0.016 0.002 PHE B 127 TRP 0.026 0.002 TRP B 598 HIS 0.006 0.002 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00548 (17646) covalent geometry : angle 0.69737 (24084) hydrogen bonds : bond 0.04914 ( 839) hydrogen bonds : angle 4.80857 ( 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 : 0.679 Fit side-chains REVERT: B 146 MET cc_start: 0.8164 (tmm) cc_final: 0.7951 (tmm) REVERT: B 200 TYR cc_start: 0.8354 (m-80) cc_final: 0.7623 (m-80) REVERT: B 354 MET cc_start: 0.8681 (pmm) cc_final: 0.8042 (pmm) REVERT: B 501 MET cc_start: 0.6897 (mpp) cc_final: 0.5880 (mpp) REVERT: B 665 MET cc_start: 0.8160 (mpp) cc_final: 0.7744 (mtt) REVERT: B 778 LEU cc_start: 0.9017 (tt) cc_final: 0.7788 (tt) REVERT: B 849 ASP cc_start: 0.8589 (p0) cc_final: 0.8229 (p0) REVERT: C 91 MET cc_start: 0.8522 (mtp) cc_final: 0.8269 (mmp) REVERT: C 240 PHE cc_start: 0.8877 (t80) cc_final: 0.8671 (t80) REVERT: C 396 MET cc_start: 0.8458 (pmm) cc_final: 0.8150 (pmm) REVERT: C 411 MET cc_start: 0.8316 (mmp) cc_final: 0.8090 (mmp) REVERT: C 508 ASP cc_start: 0.7599 (p0) cc_final: 0.7228 (p0) REVERT: C 678 LEU cc_start: 0.9031 (mt) cc_final: 0.8584 (mm) REVERT: C 738 ASP cc_start: 0.8498 (p0) cc_final: 0.8238 (p0) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1084 time to fit residues: 25.8024 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 : 0.674 ------------------------------------------------------------------------------- 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: 9.9990 chunk 50 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 164 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN 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 380 HIS C 522 HIS ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053210 restraints weight = 94504.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.054577 restraints weight = 60892.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.055559 restraints weight = 44104.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.056244 restraints weight = 34603.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056727 restraints weight = 28863.349| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17646 Z= 0.118 Angle : 0.563 9.031 24084 Z= 0.291 Chirality : 0.040 0.158 2646 Planarity : 0.004 0.072 3048 Dihedral : 13.773 130.653 2617 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % 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: -0.58 (0.19), residues: 2047 helix: 0.79 (0.16), residues: 1116 sheet: -1.03 (0.42), residues: 158 loop : -2.00 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 306 TYR 0.026 0.001 TYR B 514 PHE 0.015 0.001 PHE B 645 TRP 0.017 0.001 TRP B 598 HIS 0.009 0.001 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00253 (17646) covalent geometry : angle 0.56267 (24084) hydrogen bonds : bond 0.04300 ( 839) hydrogen bonds : angle 4.44584 ( 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 157 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: B 146 MET cc_start: 0.8115 (tmm) cc_final: 0.7909 (tmm) REVERT: B 200 TYR cc_start: 0.8311 (m-80) cc_final: 0.7970 (m-80) REVERT: B 354 MET cc_start: 0.8789 (pmm) cc_final: 0.8483 (ptp) REVERT: B 453 MET cc_start: 0.8933 (mmm) cc_final: 0.8722 (mmm) REVERT: B 501 MET cc_start: 0.6920 (mpp) cc_final: 0.6650 (mpp) REVERT: B 778 LEU cc_start: 0.8981 (tt) cc_final: 0.7905 (tt) REVERT: B 849 ASP cc_start: 0.8428 (p0) cc_final: 0.8112 (p0) REVERT: C 42 MET cc_start: 0.9446 (mmt) cc_final: 0.9238 (mmp) REVERT: C 396 MET cc_start: 0.8178 (pmm) cc_final: 0.7814 (pmm) REVERT: C 411 MET cc_start: 0.8457 (mmp) cc_final: 0.8114 (mmp) REVERT: C 508 ASP cc_start: 0.7552 (p0) cc_final: 0.7255 (p0) REVERT: C 678 LEU cc_start: 0.8994 (mt) cc_final: 0.8537 (mm) REVERT: C 738 ASP cc_start: 0.8197 (p0) cc_final: 0.7779 (p0) REVERT: C 941 MET cc_start: 0.7956 (ptt) cc_final: 0.7555 (ptt) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1068 time to fit residues: 27.9194 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 : 0.648 ------------------------------------------------------------------------------- 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: 9.9990 chunk 131 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 chunk 179 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN C 297 ASN ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.049743 restraints weight = 98729.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.051014 restraints weight = 64503.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.051912 restraints weight = 47150.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.052501 restraints weight = 37323.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.052988 restraints weight = 31574.609| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 17646 Z= 0.284 Angle : 0.737 13.511 24084 Z= 0.376 Chirality : 0.044 0.146 2646 Planarity : 0.005 0.069 3048 Dihedral : 13.800 128.752 2617 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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: -0.81 (0.18), residues: 2047 helix: 0.59 (0.16), residues: 1102 sheet: -1.30 (0.42), residues: 159 loop : -2.00 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 491 TYR 0.019 0.002 TYR B 514 PHE 0.027 0.002 PHE B 127 TRP 0.021 0.002 TRP B 187 HIS 0.009 0.002 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00625 (17646) covalent geometry : angle 0.73733 (24084) hydrogen bonds : bond 0.04896 ( 839) hydrogen bonds : angle 4.83365 ( 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 140 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.605 Fit side-chains REVERT: B 146 MET cc_start: 0.8329 (tmm) cc_final: 0.8093 (tmm) REVERT: B 200 TYR cc_start: 0.8669 (m-80) cc_final: 0.8443 (m-80) REVERT: B 354 MET cc_start: 0.8708 (pmm) cc_final: 0.8091 (pmm) REVERT: B 453 MET cc_start: 0.9062 (mmm) cc_final: 0.8752 (mmm) REVERT: B 501 MET cc_start: 0.7092 (mpp) cc_final: 0.6359 (mpp) REVERT: B 665 MET cc_start: 0.8336 (mpp) cc_final: 0.7942 (mtt) REVERT: B 778 LEU cc_start: 0.9029 (tt) cc_final: 0.8430 (tt) REVERT: B 849 ASP cc_start: 0.8283 (p0) cc_final: 0.7882 (p0) REVERT: C 396 MET cc_start: 0.8374 (pmm) cc_final: 0.8068 (pmm) REVERT: C 508 ASP cc_start: 0.7748 (p0) cc_final: 0.7391 (p0) REVERT: C 594 MET cc_start: 0.8711 (tpp) cc_final: 0.8389 (tpp) REVERT: C 678 LEU cc_start: 0.8920 (mt) cc_final: 0.8325 (mt) REVERT: C 738 ASP cc_start: 0.8185 (p0) cc_final: 0.7945 (p0) REVERT: D 5 LYS cc_start: 0.6476 (pptt) cc_final: 0.6226 (pptt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1034 time to fit residues: 24.4604 Evaluate side-chains 100 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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: 1.9990 chunk 182 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN B 281 GLN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** 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** D 65 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.061549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.051162 restraints weight = 95999.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.052477 restraints weight = 62234.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.053358 restraints weight = 45230.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054045 restraints weight = 35874.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054463 restraints weight = 29966.810| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2381 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= 0.158 Angle : 0.611 11.850 24084 Z= 0.313 Chirality : 0.041 0.172 2646 Planarity : 0.005 0.072 3048 Dihedral : 13.795 129.481 2617 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: -0.62 (0.19), residues: 2047 helix: 0.73 (0.16), residues: 1107 sheet: -1.25 (0.45), residues: 149 loop : -1.90 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 306 TYR 0.017 0.001 TYR B 514 PHE 0.014 0.001 PHE B 127 TRP 0.015 0.001 TRP B 265 HIS 0.007 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00354 (17646) covalent geometry : angle 0.61089 (24084) hydrogen bonds : bond 0.04293 ( 839) hydrogen bonds : angle 4.53017 ( 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 147 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8256 (tmm) cc_final: 0.7938 (tmm) REVERT: B 453 MET cc_start: 0.9011 (mmm) cc_final: 0.8696 (mmm) REVERT: B 778 LEU cc_start: 0.8986 (tt) cc_final: 0.8153 (tt) REVERT: B 841 LEU cc_start: 0.9142 (mt) cc_final: 0.8667 (tt) REVERT: B 849 ASP cc_start: 0.8264 (p0) cc_final: 0.7889 (p0) REVERT: C 240 PHE cc_start: 0.8853 (t80) cc_final: 0.8591 (t80) REVERT: C 508 ASP cc_start: 0.7726 (p0) cc_final: 0.7359 (p0) REVERT: C 516 LEU cc_start: 0.9200 (mt) cc_final: 0.8914 (mm) REVERT: C 697 MET cc_start: 0.8452 (mmm) cc_final: 0.8190 (mmm) REVERT: C 738 ASP cc_start: 0.8162 (p0) cc_final: 0.7809 (p0) REVERT: D 5 LYS cc_start: 0.6462 (pptt) cc_final: 0.6246 (pptt) REVERT: D 100 MET cc_start: 0.9057 (mmm) cc_final: 0.8843 (mmm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1110 time to fit residues: 26.7637 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 : 0.632 ------------------------------------------------------------------------------- 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: 0.6980 chunk 79 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 107 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN B 281 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN D 61 ASN ** D 65 HIS ** 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 = 0.3196 r_free = 0.3196 target = 0.060984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.050704 restraints weight = 96868.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051986 restraints weight = 63193.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052901 restraints weight = 46084.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.053552 restraints weight = 36413.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053968 restraints weight = 30451.645| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17646 Z= 0.181 Angle : 0.619 11.859 24084 Z= 0.319 Chirality : 0.041 0.174 2646 Planarity : 0.005 0.069 3048 Dihedral : 13.776 129.243 2617 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: -0.52 (0.19), residues: 2047 helix: 0.82 (0.16), residues: 1098 sheet: -1.11 (0.43), residues: 159 loop : -1.86 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 306 TYR 0.022 0.002 TYR B 514 PHE 0.017 0.001 PHE B 756 TRP 0.019 0.001 TRP B 187 HIS 0.008 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00403 (17646) covalent geometry : angle 0.61937 (24084) hydrogen bonds : bond 0.04249 ( 839) hydrogen bonds : angle 4.53340 ( 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 141 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: B 146 MET cc_start: 0.8299 (tmm) cc_final: 0.7968 (tmm) REVERT: B 354 MET cc_start: 0.8647 (pmm) cc_final: 0.8079 (pmm) REVERT: B 453 MET cc_start: 0.9042 (mmm) cc_final: 0.8700 (mmm) REVERT: B 501 MET cc_start: 0.7144 (mpp) cc_final: 0.6198 (mpp) REVERT: B 849 ASP cc_start: 0.8322 (p0) cc_final: 0.7931 (p0) REVERT: C 240 PHE cc_start: 0.8855 (t80) cc_final: 0.8618 (t80) REVERT: C 508 ASP cc_start: 0.7714 (p0) cc_final: 0.7376 (p0) REVERT: C 697 MET cc_start: 0.8443 (mmm) cc_final: 0.8175 (mmm) REVERT: C 738 ASP cc_start: 0.8216 (p0) cc_final: 0.7900 (p0) REVERT: D 5 LYS cc_start: 0.6497 (pptt) cc_final: 0.6257 (pptt) REVERT: D 100 MET cc_start: 0.9061 (mmm) cc_final: 0.8798 (mmm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1094 time to fit residues: 25.5089 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 : 0.666 ------------------------------------------------------------------------------- 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: 6.9990 chunk 123 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN B 281 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN ** C 681 ASN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.049325 restraints weight = 98665.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.050544 restraints weight = 64904.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.051413 restraints weight = 47629.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051973 restraints weight = 37915.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052451 restraints weight = 32208.413| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 17646 Z= 0.275 Angle : 0.753 14.554 24084 Z= 0.384 Chirality : 0.045 0.154 2646 Planarity : 0.005 0.071 3048 Dihedral : 13.867 129.362 2617 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -0.94 (0.18), residues: 2047 helix: 0.45 (0.15), residues: 1101 sheet: -1.35 (0.43), residues: 159 loop : -2.00 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 491 TYR 0.039 0.002 TYR B 280 PHE 0.024 0.002 PHE B 756 TRP 0.032 0.002 TRP B 187 HIS 0.009 0.002 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00601 (17646) covalent geometry : angle 0.75257 (24084) hydrogen bonds : bond 0.04820 ( 839) hydrogen bonds : angle 4.93822 ( 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 137 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: B 146 MET cc_start: 0.8411 (tmm) cc_final: 0.8159 (tmm) REVERT: B 200 TYR cc_start: 0.8142 (m-80) cc_final: 0.7913 (m-80) REVERT: B 354 MET cc_start: 0.8656 (pmm) cc_final: 0.8144 (pmm) REVERT: B 453 MET cc_start: 0.9112 (mmm) cc_final: 0.8756 (mmm) REVERT: B 501 MET cc_start: 0.7286 (mpp) cc_final: 0.7071 (mpp) REVERT: B 815 LEU cc_start: 0.9474 (pp) cc_final: 0.9272 (pp) REVERT: B 849 ASP cc_start: 0.8465 (p0) cc_final: 0.8137 (p0) REVERT: C 240 PHE cc_start: 0.8850 (t80) cc_final: 0.8570 (t80) REVERT: C 411 MET cc_start: 0.8477 (mmp) cc_final: 0.8192 (mmp) REVERT: C 508 ASP cc_start: 0.7709 (p0) cc_final: 0.7344 (p0) REVERT: C 697 MET cc_start: 0.8498 (mmm) cc_final: 0.8148 (mmm) REVERT: C 738 ASP cc_start: 0.8154 (p0) cc_final: 0.7858 (p0) REVERT: D 100 MET cc_start: 0.9081 (mmm) cc_final: 0.8797 (mmm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1079 time to fit residues: 24.6786 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 : 0.567 ------------------------------------------------------------------------------- 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: 0.3980 chunk 189 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 705 HIS ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS C 44 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 724 GLN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.051380 restraints weight = 95829.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.052704 restraints weight = 61919.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053634 restraints weight = 44913.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.054299 restraints weight = 35323.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054733 restraints weight = 29513.813| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17646 Z= 0.134 Angle : 0.611 10.315 24084 Z= 0.315 Chirality : 0.041 0.201 2646 Planarity : 0.005 0.072 3048 Dihedral : 13.796 129.152 2617 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -0.60 (0.19), residues: 2047 helix: 0.73 (0.16), residues: 1104 sheet: -1.28 (0.44), residues: 153 loop : -1.83 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 491 TYR 0.014 0.001 TYR B 394 PHE 0.015 0.001 PHE C 193 TRP 0.024 0.001 TRP B 187 HIS 0.006 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00295 (17646) covalent geometry : angle 0.61069 (24084) hydrogen bonds : bond 0.04136 ( 839) hydrogen bonds : angle 4.53809 ( 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 148 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8323 (tmm) cc_final: 0.8038 (tmm) REVERT: B 200 TYR cc_start: 0.8025 (m-80) cc_final: 0.7808 (m-80) REVERT: B 453 MET cc_start: 0.9043 (mmm) cc_final: 0.8690 (mmm) REVERT: B 499 MET cc_start: 0.7904 (ttm) cc_final: 0.7251 (mtp) REVERT: B 501 MET cc_start: 0.7125 (mpp) cc_final: 0.6485 (mpp) REVERT: B 841 LEU cc_start: 0.9123 (mt) cc_final: 0.8828 (tt) REVERT: B 849 ASP cc_start: 0.8377 (p0) cc_final: 0.8085 (p0) REVERT: C 240 PHE cc_start: 0.8834 (t80) cc_final: 0.8509 (t80) REVERT: C 508 ASP cc_start: 0.7592 (p0) cc_final: 0.7202 (p0) REVERT: C 697 MET cc_start: 0.8338 (mmm) cc_final: 0.7995 (mmm) REVERT: C 738 ASP cc_start: 0.8106 (p0) cc_final: 0.7731 (p0) REVERT: C 941 MET cc_start: 0.7792 (ptt) cc_final: 0.7442 (ptt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1044 time to fit residues: 26.3655 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 : 0.593 ------------------------------------------------------------------------------- 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: 2.9990 chunk 81 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 163 optimal weight: 0.0970 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.050991 restraints weight = 96118.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.052311 restraints weight = 62185.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.053237 restraints weight = 45070.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053873 restraints weight = 35429.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.054269 restraints weight = 29686.705| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17646 Z= 0.148 Angle : 0.610 10.596 24084 Z= 0.314 Chirality : 0.042 0.181 2646 Planarity : 0.005 0.070 3048 Dihedral : 13.728 128.710 2617 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -0.49 (0.19), residues: 2047 helix: 0.79 (0.16), residues: 1104 sheet: -1.16 (0.44), residues: 148 loop : -1.76 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 491 TYR 0.014 0.001 TYR B 394 PHE 0.020 0.001 PHE B 64 TRP 0.031 0.001 TRP B 187 HIS 0.007 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00331 (17646) covalent geometry : angle 0.61011 (24084) hydrogen bonds : bond 0.04059 ( 839) hydrogen bonds : angle 4.52526 ( 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 141 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8290 (tmm) cc_final: 0.8015 (tmm) REVERT: B 453 MET cc_start: 0.9046 (mmm) cc_final: 0.8732 (mmm) REVERT: B 469 MET cc_start: 0.8440 (mtp) cc_final: 0.8225 (mtm) REVERT: B 499 MET cc_start: 0.7867 (ttm) cc_final: 0.7659 (mtp) REVERT: B 604 MET cc_start: 0.7636 (ttt) cc_final: 0.7344 (ttt) REVERT: B 841 LEU cc_start: 0.9148 (mt) cc_final: 0.8877 (tt) REVERT: B 849 ASP cc_start: 0.8368 (p0) cc_final: 0.8090 (p0) REVERT: C 240 PHE cc_start: 0.8875 (t80) cc_final: 0.8594 (t80) REVERT: C 508 ASP cc_start: 0.7536 (p0) cc_final: 0.7180 (p0) REVERT: C 678 LEU cc_start: 0.8904 (mm) cc_final: 0.8686 (mm) REVERT: C 697 MET cc_start: 0.8407 (mmm) cc_final: 0.8043 (mmm) REVERT: C 738 ASP cc_start: 0.8042 (p0) cc_final: 0.7632 (p0) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1024 time to fit residues: 24.5848 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 : 0.582 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 155 optimal weight: 0.0270 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 162 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 = 0.3236 r_free = 0.3236 target = 0.062458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.052069 restraints weight = 94838.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.053418 restraints weight = 60975.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.054376 restraints weight = 44015.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055010 restraints weight = 34523.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055523 restraints weight = 28942.922| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17646 Z= 0.118 Angle : 0.597 9.016 24084 Z= 0.304 Chirality : 0.041 0.178 2646 Planarity : 0.004 0.071 3048 Dihedral : 13.685 127.850 2617 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % 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: -0.38 (0.19), residues: 2047 helix: 0.89 (0.16), residues: 1106 sheet: -1.00 (0.45), residues: 148 loop : -1.75 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 306 TYR 0.014 0.001 TYR B 280 PHE 0.018 0.001 PHE B 756 TRP 0.030 0.001 TRP B 187 HIS 0.006 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00259 (17646) covalent geometry : angle 0.59654 (24084) hydrogen bonds : bond 0.03841 ( 839) hydrogen bonds : angle 4.39081 ( 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 148 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8215 (tmm) cc_final: 0.7935 (tmm) REVERT: B 453 MET cc_start: 0.9027 (mmm) cc_final: 0.8708 (mmm) REVERT: B 469 MET cc_start: 0.8416 (mtp) cc_final: 0.8187 (mtm) REVERT: B 499 MET cc_start: 0.7891 (ttm) cc_final: 0.7245 (mtp) REVERT: B 501 MET cc_start: 0.7111 (mpp) cc_final: 0.6642 (mpp) REVERT: B 604 MET cc_start: 0.7622 (ttt) cc_final: 0.7378 (ttt) REVERT: B 841 LEU cc_start: 0.9193 (mt) cc_final: 0.8943 (tt) REVERT: B 849 ASP cc_start: 0.8363 (p0) cc_final: 0.8121 (p0) REVERT: C 240 PHE cc_start: 0.8811 (t80) cc_final: 0.8563 (t80) REVERT: C 385 GLU cc_start: 0.8748 (tt0) cc_final: 0.7814 (tp30) REVERT: C 411 MET cc_start: 0.8237 (mmm) cc_final: 0.7946 (mmm) REVERT: C 508 ASP cc_start: 0.7515 (p0) cc_final: 0.7122 (p0) REVERT: C 697 MET cc_start: 0.8336 (mmm) cc_final: 0.7960 (mmm) REVERT: C 738 ASP cc_start: 0.8014 (p0) cc_final: 0.7572 (p0) REVERT: C 941 MET cc_start: 0.7865 (ptt) cc_final: 0.7576 (ptt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1028 time to fit residues: 25.7036 Evaluate side-chains 107 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 10.0000 chunk 156 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN C 881 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.050086 restraints weight = 97602.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051370 restraints weight = 63629.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.052268 restraints weight = 46165.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052911 restraints weight = 36429.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.053344 restraints weight = 30517.445| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 17646 Z= 0.234 Angle : 0.693 12.710 24084 Z= 0.354 Chirality : 0.043 0.180 2646 Planarity : 0.005 0.063 3048 Dihedral : 13.725 127.675 2617 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -0.58 (0.19), residues: 2047 helix: 0.72 (0.16), residues: 1097 sheet: -1.22 (0.43), residues: 153 loop : -1.77 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 503 TYR 0.018 0.002 TYR B 394 PHE 0.022 0.002 PHE B 64 TRP 0.033 0.002 TRP B 187 HIS 0.007 0.002 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00520 (17646) covalent geometry : angle 0.69266 (24084) hydrogen bonds : bond 0.04384 ( 839) hydrogen bonds : angle 4.69590 ( 2454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2010.94 seconds wall clock time: 35 minutes 51.68 seconds (2151.68 seconds total)