Starting phenix.real_space_refine on Sat Aug 8 01:02:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u3k_41865/08_2026/8u3k_41865.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u3k_41865/08_2026/8u3k_41865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u3k_41865/08_2026/8u3k_41865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u3k_41865/08_2026/8u3k_41865.map" model { file = "/net/cci-nas-00/data/ceres_data/8u3k_41865/08_2026/8u3k_41865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u3k_41865/08_2026/8u3k_41865.cif" } resolution = 2.5 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 15723 2.51 5 N 4282 2.21 5 O 4869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 243 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24990 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9279 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1116} Chain breaks: 4 Chain: "C" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 582 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 5453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5453 Classifications: {'peptide': 669} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 634} Chain breaks: 2 Chain: "F" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 9142 Classifications: {'peptide': 1133} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1099} Chain breaks: 6 Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 220 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.67, per 1000 atoms: 0.19 Number of scatterers: 24990 At special positions: 0 Unit cell: (139.144, 153.309, 159.141, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 55 15.00 Mg 1 11.99 O 4869 8.00 N 4282 7.00 C 15723 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: 1.88 Conformation dependent library (CDL) restraints added in 965.8 milliseconds 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 31 sheets defined 51.1% alpha, 13.7% beta 10 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 54 through 77 Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.829A pdb=" N CYS A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 161 removed outlier: 3.732A pdb=" N ALA A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 161' Processing helix chain 'A' and resid 162 through 178 removed outlier: 4.220A pdb=" N HIS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 209 removed outlier: 4.011A pdb=" N GLY A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.142A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 264 removed outlier: 4.230A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.516A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.566A pdb=" N ASP A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.687A pdb=" N LEU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 400 through 428 removed outlier: 4.015A pdb=" N ARG A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 4.390A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 524 through 536 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 636 through 656 removed outlier: 3.560A pdb=" N LYS A 646 " --> pdb=" O SER A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 694 removed outlier: 3.709A pdb=" N PHE A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.541A pdb=" N SER A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.544A pdb=" N GLU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 747 through 752' Processing helix chain 'A' and resid 789 through 794 removed outlier: 4.288A pdb=" N ASN A 793 " --> pdb=" O HIS A 790 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 808 removed outlier: 4.166A pdb=" N ILE A 801 " --> pdb=" O GLN A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 Processing helix chain 'A' and resid 827 through 837 removed outlier: 3.899A pdb=" N GLN A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 856 removed outlier: 3.940A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.314A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 901 Processing helix chain 'A' and resid 909 through 938 removed outlier: 3.912A pdb=" N ARG A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 931 " --> pdb=" O MET A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.885A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1013 removed outlier: 3.629A pdb=" N CYS A1013 " --> pdb=" O GLU A1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1010 through 1013' Processing helix chain 'A' and resid 1014 through 1021 removed outlier: 3.875A pdb=" N ASN A1021 " --> pdb=" O THR A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.763A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1068 removed outlier: 3.951A pdb=" N ALA A1068 " --> pdb=" O ALA A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1127 removed outlier: 3.716A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'E' and resid 45 through 50 removed outlier: 4.323A pdb=" N LYS E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 62 removed outlier: 4.263A pdb=" N GLY E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 184 through 187 Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 249 through 266 removed outlier: 3.775A pdb=" N LYS E 262 " --> pdb=" O MET E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 297 Processing helix chain 'E' and resid 298 through 301 Processing helix chain 'E' and resid 317 through 329 removed outlier: 3.720A pdb=" N THR E 321 " --> pdb=" O ASP E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 391 through 411 removed outlier: 3.736A pdb=" N VAL E 395 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 473 removed outlier: 3.811A pdb=" N ASP E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 476 No H-bonds generated for 'chain 'E' and resid 474 through 476' Processing helix chain 'E' and resid 477 through 482 Processing helix chain 'E' and resid 511 through 527 Processing helix chain 'E' and resid 531 through 542 removed outlier: 3.719A pdb=" N LEU E 535 " --> pdb=" O PRO E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 558 Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.616A pdb=" N SER E 570 " --> pdb=" O ASP E 567 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR E 571 " --> pdb=" O GLU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 589 Processing helix chain 'E' and resid 649 through 657 Processing helix chain 'E' and resid 670 through 687 removed outlier: 3.917A pdb=" N LYS E 674 " --> pdb=" O PRO E 670 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS E 675 " --> pdb=" O TYR E 671 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE E 685 " --> pdb=" O GLU E 681 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG E 686 " --> pdb=" O MET E 682 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 687 " --> pdb=" O GLN E 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 20 through 38 removed outlier: 3.676A pdb=" N ILE F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 77 Processing helix chain 'F' and resid 78 through 81 removed outlier: 3.550A pdb=" N GLY F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 81' Processing helix chain 'F' and resid 94 through 112 Processing helix chain 'F' and resid 121 through 131 Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.770A pdb=" N CYS F 145 " --> pdb=" O GLN F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 157 Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.910A pdb=" N ALA F 161 " --> pdb=" O ASN F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 177 Processing helix chain 'F' and resid 181 through 209 Processing helix chain 'F' and resid 216 through 227 Processing helix chain 'F' and resid 228 through 234 removed outlier: 4.071A pdb=" N ILE F 232 " --> pdb=" O PRO F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 259 through 264 removed outlier: 4.030A pdb=" N LEU F 264 " --> pdb=" O LEU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 287 removed outlier: 3.572A pdb=" N LYS F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 304 Processing helix chain 'F' and resid 312 through 316 removed outlier: 3.553A pdb=" N ASP F 316 " --> pdb=" O PRO F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 337 Proline residue: F 324 - end of helix Processing helix chain 'F' and resid 401 through 428 Processing helix chain 'F' and resid 445 through 459 removed outlier: 4.294A pdb=" N GLN F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU F 450 " --> pdb=" O GLY F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'F' and resid 464 through 472 Processing helix chain 'F' and resid 493 through 497 removed outlier: 3.530A pdb=" N HIS F 496 " --> pdb=" O SER F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 556 through 565 Processing helix chain 'F' and resid 572 through 587 Processing helix chain 'F' and resid 604 through 616 Processing helix chain 'F' and resid 621 through 629 Processing helix chain 'F' and resid 636 through 656 removed outlier: 4.005A pdb=" N LYS F 646 " --> pdb=" O SER F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 674 No H-bonds generated for 'chain 'F' and resid 672 through 674' Processing helix chain 'F' and resid 675 through 694 removed outlier: 3.508A pdb=" N PHE F 681 " --> pdb=" O ASN F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 711 Processing helix chain 'F' and resid 713 through 723 removed outlier: 3.505A pdb=" N SER F 717 " --> pdb=" O TYR F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 removed outlier: 3.952A pdb=" N GLY F 752 " --> pdb=" O LEU F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 793 removed outlier: 4.188A pdb=" N ASN F 793 " --> pdb=" O HIS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 794 through 807 removed outlier: 3.556A pdb=" N GLN F 800 " --> pdb=" O CYS F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 811 through 824 Processing helix chain 'F' and resid 827 through 836 Processing helix chain 'F' and resid 838 through 856 removed outlier: 4.135A pdb=" N GLN F 842 " --> pdb=" O THR F 838 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 856 " --> pdb=" O ALA F 852 " (cutoff:3.500A) Processing helix chain 'F' and resid 873 through 880 removed outlier: 4.494A pdb=" N ILE F 877 " --> pdb=" O GLY F 873 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU F 880 " --> pdb=" O GLU F 876 " (cutoff:3.500A) Processing helix chain 'F' and resid 884 through 888 removed outlier: 4.306A pdb=" N LEU F 887 " --> pdb=" O ASP F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 889 through 901 Processing helix chain 'F' and resid 909 through 939 removed outlier: 3.724A pdb=" N ARG F 913 " --> pdb=" O ASP F 909 " (cutoff:3.500A) Processing helix chain 'F' and resid 943 through 960 Processing helix chain 'F' and resid 970 through 972 No H-bonds generated for 'chain 'F' and resid 970 through 972' Processing helix chain 'F' and resid 1010 through 1013 removed outlier: 3.640A pdb=" N CYS F1013 " --> pdb=" O GLU F1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1010 through 1013' Processing helix chain 'F' and resid 1014 through 1020 Processing helix chain 'F' and resid 1023 through 1032 removed outlier: 3.689A pdb=" N TRP F1027 " --> pdb=" O TYR F1023 " (cutoff:3.500A) Processing helix chain 'F' and resid 1045 through 1052 Processing helix chain 'F' and resid 1052 through 1068 removed outlier: 3.660A pdb=" N ALA F1068 " --> pdb=" O ALA F1064 " (cutoff:3.500A) Processing helix chain 'F' and resid 1113 through 1127 removed outlier: 3.701A pdb=" N GLU F1125 " --> pdb=" O LEU F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1176 through 1189 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 47 removed outlier: 6.344A pdb=" N TYR A 89 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP A 272 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 91 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 345 removed outlier: 6.423A pdb=" N ALA A 341 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE A 385 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N SER A 387 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLU A 345 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 382 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 388 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 371 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.075A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 664 " --> pdb=" O TYR A 775 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 697 through 698 Processing sheet with id=AA8, first strand: chain 'A' and resid 744 through 745 Processing sheet with id=AA9, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AB1, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.681A pdb=" N ASN A1042 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 983 through 985 Processing sheet with id=AB3, first strand: chain 'A' and resid 1071 through 1074 removed outlier: 3.535A pdb=" N ASN A1086 " --> pdb=" O LEU A1099 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1137 through 1138 removed outlier: 3.596A pdb=" N GLY A1138 " --> pdb=" O ILE A1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 269 through 275 removed outlier: 6.675A pdb=" N SER E 270 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE E 21 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS E 272 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU E 17 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 14 " --> pdb=" O LEU E 509 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN E 507 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N ILE E 18 " --> pdb=" O GLY E 505 " (cutoff:3.500A) removed outlier: 13.642A pdb=" N GLY E 505 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 19.976A pdb=" N GLN E 20 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ASP E 503 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 30.626A pdb=" N SER E 22 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 34.208A pdb=" N PHE E 501 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU E 638 " --> pdb=" O THR E 504 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE E 506 " --> pdb=" O SER E 636 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER E 636 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS E 637 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA E 622 " --> pdb=" O HIS E 637 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 269 through 275 removed outlier: 6.675A pdb=" N SER E 270 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE E 21 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS E 272 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU E 17 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 14 " --> pdb=" O LEU E 509 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN E 507 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N ILE E 18 " --> pdb=" O GLY E 505 " (cutoff:3.500A) removed outlier: 13.642A pdb=" N GLY E 505 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 19.976A pdb=" N GLN E 20 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ASP E 503 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 30.626A pdb=" N SER E 22 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 34.208A pdb=" N PHE E 501 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 66 through 69 removed outlier: 3.677A pdb=" N CYS E 66 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE E 34 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 136 through 144 removed outlier: 6.384A pdb=" N TYR E 137 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE E 159 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU E 139 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL E 157 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N TYR E 152 " --> pdb=" O PRO E 182 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 236 through 237 Processing sheet with id=AC1, first strand: chain 'E' and resid 334 through 336 removed outlier: 6.618A pdb=" N LEU E 305 " --> pdb=" O GLU E 334 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA E 336 " --> pdb=" O LEU E 305 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE E 307 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 43 through 47 removed outlier: 6.110A pdb=" N ALA F 43 " --> pdb=" O ILE F 539 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY F 541 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU F 45 " --> pdb=" O GLY F 541 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR F 89 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP F 272 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 91 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU F 88 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU F 242 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR F 90 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AC4, first strand: chain 'F' and resid 251 through 252 Processing sheet with id=AC5, first strand: chain 'F' and resid 291 through 292 Processing sheet with id=AC6, first strand: chain 'F' and resid 342 through 345 removed outlier: 6.766A pdb=" N ASN F 343 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N SER F 387 " --> pdb=" O ASN F 343 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLU F 345 " --> pdb=" O SER F 387 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP F 388 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS F 371 " --> pdb=" O ASP F 388 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 595 through 601 removed outlier: 6.477A pdb=" N VAL F 595 " --> pdb=" O ILE F 866 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU F 868 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR F 597 " --> pdb=" O LEU F 868 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL F 870 " --> pdb=" O THR F 597 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS F 599 " --> pdb=" O VAL F 870 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE F 774 " --> pdb=" O PHE F 869 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP F 871 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU F 776 " --> pdb=" O ASP F 871 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS F 698 " --> pdb=" O VAL F 728 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE F 730 " --> pdb=" O LYS F 698 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 700 " --> pdb=" O PHE F 730 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N THR F 732 " --> pdb=" O PHE F 700 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 744 through 745 Processing sheet with id=AC9, first strand: chain 'F' and resid 755 through 757 Processing sheet with id=AD1, first strand: chain 'F' and resid 962 through 963 removed outlier: 3.692A pdb=" N ASN F1042 " --> pdb=" O VAL F 963 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 983 through 985 Processing sheet with id=AD3, first strand: chain 'F' and resid 1071 through 1074 removed outlier: 6.670A pdb=" N TRP F1098 " --> pdb=" O ILE F1132 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL F1134 " --> pdb=" O TRP F1098 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASP F1100 " --> pdb=" O VAL F1134 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 1137 through 1138 1175 hydrogen bonds defined for protein. 3327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7273 1.33 - 1.46: 5911 1.46 - 1.58: 12229 1.58 - 1.71: 104 1.71 - 1.83: 93 Bond restraints: 25610 Sorted by residual: bond pdb=" C1' DC C 18 " pdb=" N1 DC C 18 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.18e+01 bond pdb=" C3' DT G 31 " pdb=" O3' DT G 31 " ideal model delta sigma weight residual 1.435 1.379 0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" C3' DG D 7 " pdb=" O3' DG D 7 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.43e+01 bond pdb=" C3' DT G 28 " pdb=" C2' DT G 28 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA D 4 " pdb=" O3' DA D 4 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 25605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 34569 3.31 - 6.62: 252 6.62 - 9.93: 20 9.93 - 13.24: 5 13.24 - 16.55: 5 Bond angle restraints: 34851 Sorted by residual: angle pdb=" N GLU E 132 " pdb=" CA GLU E 132 " pdb=" C GLU E 132 " ideal model delta sigma weight residual 110.61 103.31 7.30 1.25e+00 6.40e-01 3.41e+01 angle pdb=" CA ILE F1119 " pdb=" CB ILE F1119 " pdb=" CG1 ILE F1119 " ideal model delta sigma weight residual 110.40 120.05 -9.65 1.70e+00 3.46e-01 3.22e+01 angle pdb=" CB LYS F 111 " pdb=" CG LYS F 111 " pdb=" CD LYS F 111 " ideal model delta sigma weight residual 111.30 123.67 -12.37 2.30e+00 1.89e-01 2.89e+01 angle pdb=" CB MET A 824 " pdb=" CG MET A 824 " pdb=" SD MET A 824 " ideal model delta sigma weight residual 112.70 127.55 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" O4' DC C 18 " pdb=" C1' DC C 18 " pdb=" N1 DC C 18 " ideal model delta sigma weight residual 108.00 111.36 -3.36 7.00e-01 2.04e+00 2.30e+01 ... (remaining 34846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 14621 34.87 - 69.74: 635 69.74 - 104.61: 33 104.61 - 139.48: 0 139.48 - 174.35: 1 Dihedral angle restraints: 15290 sinusoidal: 6614 harmonic: 8676 Sorted by residual: dihedral pdb=" CA PHE F 999 " pdb=" C PHE F 999 " pdb=" N ASP F1000 " pdb=" CA ASP F1000 " ideal model delta harmonic sigma weight residual -180.00 -138.64 -41.36 0 5.00e+00 4.00e-02 6.84e+01 dihedral pdb=" CA PHE A 999 " pdb=" C PHE A 999 " pdb=" N ASP A1000 " pdb=" CA ASP A1000 " ideal model delta harmonic sigma weight residual -180.00 -140.48 -39.52 0 5.00e+00 4.00e-02 6.25e+01 dihedral pdb=" CA TYR F 788 " pdb=" C TYR F 788 " pdb=" N SER F 789 " pdb=" CA SER F 789 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 15287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2433 0.041 - 0.082: 989 0.082 - 0.123: 334 0.123 - 0.164: 74 0.164 - 0.205: 7 Chirality restraints: 3837 Sorted by residual: chirality pdb=" CA PRO E 380 " pdb=" N PRO E 380 " pdb=" C PRO E 380 " pdb=" CB PRO E 380 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE F 53 " pdb=" CA ILE F 53 " pdb=" CG1 ILE F 53 " pdb=" CG2 ILE F 53 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CA ASP E 330 " pdb=" N ASP E 330 " pdb=" C ASP E 330 " pdb=" CB ASP E 330 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 3834 not shown) Planarity restraints: 4321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 379 " -0.065 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO E 380 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO E 380 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 380 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 131 " -0.035 2.00e-02 2.50e+03 2.59e-02 1.17e+01 pdb=" CG PHE E 131 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE E 131 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE E 131 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 131 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 131 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 131 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1076 " -0.050 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO A1077 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " -0.041 5.00e-02 4.00e+02 ... (remaining 4318 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 222 2.59 - 3.17: 20893 3.17 - 3.75: 39604 3.75 - 4.32: 57429 4.32 - 4.90: 93102 Nonbonded interactions: 211250 Sorted by model distance: nonbonded pdb=" OP1 DA D 3 " pdb="MG MG D 101 " model vdw 2.016 2.170 nonbonded pdb=" OE1 GLN F 291 " pdb=" OH TYR F 413 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR A 983 " pdb=" O MET A1044 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR F 983 " pdb=" O MET F1044 " model vdw 2.214 3.040 nonbonded pdb=" O VAL E 28 " pdb=" N ARG E 30 " model vdw 2.221 3.120 ... (remaining 211245 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 388 or resid 400 through 473 or resid 487 throug \ h 762 or resid 767 through 1190)) selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.860 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 : 0.009 0.083 25610 Z= 0.418 Angle : 0.845 16.551 34851 Z= 0.516 Chirality : 0.050 0.205 3837 Planarity : 0.005 0.095 4321 Dihedral : 17.428 174.352 9668 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.11 % Favored : 96.75 % Rotamer: Outliers : 1.60 % Allowed : 15.34 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.09 (0.15), residues: 2922 helix: 0.75 (0.14), residues: 1323 sheet: -0.12 (0.25), residues: 419 loop : -0.55 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A1145 TYR 0.024 0.002 TYR A 848 PHE 0.055 0.003 PHE E 131 TRP 0.036 0.003 TRP F1098 HIS 0.009 0.001 HIS A 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00851 / 0.42 (25610) covalent geometry : angle 0.84538 / 0.52 (34851) hydrogen bonds : bond 0.17746 / 11.86 ( 1191) hydrogen bonds : angle 6.98729 / 4.88 ( 3367) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8444 (mtmp) cc_final: 0.8168 (mtmm) REVERT: A 1067 THR cc_start: 0.9113 (t) cc_final: 0.8912 (m) REVERT: A 1145 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7551 (ttm-80) REVERT: E 328 HIS cc_start: 0.9100 (OUTLIER) cc_final: 0.8851 (m-70) REVERT: F 939 ASN cc_start: 0.8196 (m-40) cc_final: 0.7796 (p0) outliers start: 42 outliers final: 27 residues processed: 182 average time/residue: 0.5769 time to fit residues: 122.1349 Evaluate side-chains 162 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 353 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 607 PHE Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1137 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.0020 chunk 111 optimal weight: 7.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 836 HIS A1020 GLN E 328 HIS ** E 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 781 GLN F 940 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.082275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.057828 restraints weight = 71177.181| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.46 r_work: 0.3052 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25610 Z= 0.137 Angle : 0.592 9.107 34851 Z= 0.322 Chirality : 0.042 0.221 3837 Planarity : 0.004 0.048 4321 Dihedral : 14.145 171.720 3848 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.40 % Favored : 97.47 % Rotamer: Outliers : 2.90 % Allowed : 13.39 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 2922 helix: 1.59 (0.14), residues: 1348 sheet: -0.06 (0.25), residues: 418 loop : -0.45 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1083 TYR 0.015 0.001 TYR F1081 PHE 0.030 0.001 PHE E 131 TRP 0.028 0.001 TRP F 643 HIS 0.010 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (25610) covalent geometry : angle 0.59157 / 0.32 (34851) hydrogen bonds : bond 0.04844 / 3.10 ( 1191) hydrogen bonds : angle 5.02931 / 3.52 ( 3367) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 138 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8616 (mtmp) cc_final: 0.8259 (mtmp) REVERT: A 214 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8443 (tm) REVERT: A 939 ASN cc_start: 0.8209 (t0) cc_final: 0.7642 (p0) REVERT: E 130 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7006 (pmm-80) REVERT: E 625 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8204 (pmtt) REVERT: F 119 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8844 (tpp80) REVERT: F 177 ARG cc_start: 0.8619 (mmt-90) cc_final: 0.8191 (mmp80) REVERT: F 208 LYS cc_start: 0.8553 (tptt) cc_final: 0.8205 (tppt) REVERT: F 507 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8331 (m110) REVERT: F 927 MET cc_start: 0.8870 (mtp) cc_final: 0.8607 (mtm) REVERT: F 939 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7695 (p0) outliers start: 76 outliers final: 31 residues processed: 201 average time/residue: 0.6231 time to fit residues: 145.1284 Evaluate side-chains 161 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 625 LYS Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 507 ASN Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1137 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 176 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 143 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 221 optimal weight: 0.0970 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 HIS A 291 GLN A 507 ASN A 515 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 683 GLN F 794 GLN F 951 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.081816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057232 restraints weight = 71408.060| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.46 r_work: 0.3036 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25610 Z= 0.178 Angle : 0.570 8.590 34851 Z= 0.308 Chirality : 0.042 0.157 3837 Planarity : 0.004 0.043 4321 Dihedral : 14.090 168.797 3835 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.94 % Allowed : 13.74 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.04 (0.15), residues: 2922 helix: 1.91 (0.14), residues: 1352 sheet: -0.05 (0.25), residues: 426 loop : -0.45 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 382 TYR 0.017 0.001 TYR F 788 PHE 0.028 0.002 PHE A 607 TRP 0.023 0.001 TRP F 643 HIS 0.008 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (25610) covalent geometry : angle 0.57045 / 0.31 (34851) hydrogen bonds : bond 0.04493 / 2.91 ( 1191) hydrogen bonds : angle 4.69902 / 3.29 ( 3367) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 140 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8623 (mtmp) cc_final: 0.8289 (mtmp) REVERT: A 208 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8381 (ptpp) REVERT: A 214 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8433 (tm) REVERT: A 511 ARG cc_start: 0.8032 (pmm-80) cc_final: 0.7330 (tmm160) REVERT: A 939 ASN cc_start: 0.8205 (t0) cc_final: 0.7605 (p0) REVERT: A 1087 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8103 (mmm-85) REVERT: A 1145 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7796 (ttm-80) REVERT: E 130 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.6841 (pmm-80) REVERT: E 428 MET cc_start: 0.8392 (ttm) cc_final: 0.8077 (ttp) REVERT: F 177 ARG cc_start: 0.8633 (mmt-90) cc_final: 0.8177 (mmp80) REVERT: F 201 ASP cc_start: 0.8918 (t0) cc_final: 0.8655 (t0) REVERT: F 208 LYS cc_start: 0.8545 (tptt) cc_final: 0.8283 (tppt) REVERT: F 507 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8331 (m110) REVERT: F 629 TYR cc_start: 0.7647 (m-80) cc_final: 0.7428 (m-80) REVERT: F 927 MET cc_start: 0.8866 (mtp) cc_final: 0.8624 (mtm) REVERT: F 939 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7578 (p0) REVERT: F 963 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8458 (m) outliers start: 77 outliers final: 31 residues processed: 207 average time/residue: 0.5946 time to fit residues: 143.6719 Evaluate side-chains 171 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 507 ASN Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 206 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 293 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 286 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 ASN A 821 GLN A1020 GLN A1135 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS ** F 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 694 ASN F 951 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.080671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055869 restraints weight = 71407.223| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.45 r_work: 0.2998 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 25610 Z= 0.332 Angle : 0.650 8.801 34851 Z= 0.346 Chirality : 0.046 0.170 3837 Planarity : 0.004 0.055 4321 Dihedral : 14.176 167.753 3829 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.58 % Rotamer: Outliers : 2.75 % Allowed : 14.80 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.92 (0.15), residues: 2922 helix: 1.87 (0.14), residues: 1346 sheet: -0.21 (0.24), residues: 450 loop : -0.54 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 969 TYR 0.019 0.002 TYR F 788 PHE 0.034 0.002 PHE A 607 TRP 0.037 0.002 TRP A1098 HIS 0.013 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00770 / 0.33 (25610) covalent geometry : angle 0.65048 / 0.35 (34851) hydrogen bonds : bond 0.04857 / 3.16 ( 1191) hydrogen bonds : angle 4.72589 / 3.31 ( 3367) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 140 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8623 (mtmp) cc_final: 0.8262 (mtmp) REVERT: A 214 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8490 (tm) REVERT: A 397 GLU cc_start: -0.4428 (OUTLIER) cc_final: -0.5136 (pm20) REVERT: A 511 ARG cc_start: 0.8144 (pmm-80) cc_final: 0.7466 (tmm160) REVERT: A 939 ASN cc_start: 0.8216 (t0) cc_final: 0.7575 (p0) REVERT: E 130 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.6921 (pmm-80) REVERT: F 172 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9014 (mm) REVERT: F 177 ARG cc_start: 0.8649 (mmt-90) cc_final: 0.8188 (mmp80) REVERT: F 208 LYS cc_start: 0.8548 (tptt) cc_final: 0.8324 (tppt) REVERT: F 540 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8930 (mp) REVERT: F 927 MET cc_start: 0.8891 (mtp) cc_final: 0.8652 (mtm) REVERT: F 939 ASN cc_start: 0.8160 (m-40) cc_final: 0.7670 (p0) REVERT: F 963 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8449 (m) outliers start: 72 outliers final: 36 residues processed: 203 average time/residue: 0.5805 time to fit residues: 138.0441 Evaluate side-chains 174 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1178 THR Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 387 SER Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 263 optimal weight: 0.6980 chunk 269 optimal weight: 0.0270 chunk 187 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN ** F 70 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 = 0.3769 r_free = 0.3769 target = 0.082156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057706 restraints weight = 70707.389| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.43 r_work: 0.3050 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25610 Z= 0.130 Angle : 0.552 14.416 34851 Z= 0.297 Chirality : 0.041 0.159 3837 Planarity : 0.004 0.045 4321 Dihedral : 14.109 166.624 3829 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.64 % Favored : 97.23 % Rotamer: Outliers : 2.21 % Allowed : 15.41 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.20 (0.16), residues: 2922 helix: 2.10 (0.14), residues: 1349 sheet: 0.03 (0.25), residues: 411 loop : -0.44 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1145 TYR 0.017 0.001 TYR F1081 PHE 0.025 0.001 PHE E 131 TRP 0.023 0.001 TRP F 643 HIS 0.005 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (25610) covalent geometry : angle 0.55167 / 0.30 (34851) hydrogen bonds : bond 0.03950 / 2.55 ( 1191) hydrogen bonds : angle 4.45433 / 3.12 ( 3367) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 134 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8728 (t0) cc_final: 0.8495 (t0) REVERT: A 205 LYS cc_start: 0.8626 (mtmp) cc_final: 0.8250 (mtmp) REVERT: A 206 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8256 (ttpt) REVERT: A 214 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8432 (tm) REVERT: A 511 ARG cc_start: 0.8094 (pmm-80) cc_final: 0.7433 (tmm160) REVERT: A 939 ASN cc_start: 0.8237 (t0) cc_final: 0.7611 (p0) REVERT: A 1098 TRP cc_start: 0.8808 (m100) cc_final: 0.8586 (m100) REVERT: A 1145 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7778 (ttm-80) REVERT: E 328 HIS cc_start: 0.8638 (m-70) cc_final: 0.8341 (m-70) REVERT: E 428 MET cc_start: 0.8448 (ttm) cc_final: 0.8150 (ttp) REVERT: F 177 ARG cc_start: 0.8604 (mmt-90) cc_final: 0.8127 (mmp80) REVERT: F 208 LYS cc_start: 0.8496 (tptt) cc_final: 0.8271 (tppt) REVERT: F 349 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6926 (tm) REVERT: F 629 TYR cc_start: 0.7574 (m-80) cc_final: 0.7354 (m-80) REVERT: F 663 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.7823 (ttt) REVERT: F 927 MET cc_start: 0.8879 (mtp) cc_final: 0.8654 (mtm) REVERT: F 939 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7624 (p0) REVERT: F 963 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8388 (m) REVERT: F 1093 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.6066 (tt) REVERT: F 1186 TRP cc_start: 0.8099 (t60) cc_final: 0.7535 (t60) outliers start: 58 outliers final: 31 residues processed: 182 average time/residue: 0.6576 time to fit residues: 139.1956 Evaluate side-chains 166 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 663 MET Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1093 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 112 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 201 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 GLN A1135 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.081869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057354 restraints weight = 71141.043| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.44 r_work: 0.3042 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25610 Z= 0.163 Angle : 0.554 14.128 34851 Z= 0.297 Chirality : 0.041 0.159 3837 Planarity : 0.004 0.045 4321 Dihedral : 14.081 166.143 3828 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.02 % Rotamer: Outliers : 2.10 % Allowed : 15.91 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.29 (0.16), residues: 2922 helix: 2.23 (0.14), residues: 1337 sheet: 0.02 (0.25), residues: 434 loop : -0.43 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 177 TYR 0.017 0.001 TYR F 788 PHE 0.026 0.001 PHE A 607 TRP 0.021 0.001 TRP F 643 HIS 0.006 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (25610) covalent geometry : angle 0.55351 / 0.30 (34851) hydrogen bonds : bond 0.03968 / 2.57 ( 1191) hydrogen bonds : angle 4.43279 / 3.11 ( 3367) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 136 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8738 (t0) cc_final: 0.8494 (t0) REVERT: A 205 LYS cc_start: 0.8630 (mtmp) cc_final: 0.8267 (mtmp) REVERT: A 214 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8440 (tm) REVERT: A 511 ARG cc_start: 0.8114 (pmm-80) cc_final: 0.7448 (tmm160) REVERT: A 939 ASN cc_start: 0.8229 (t0) cc_final: 0.7601 (p0) REVERT: F 172 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9017 (mm) REVERT: F 177 ARG cc_start: 0.8608 (mmt-90) cc_final: 0.8128 (mmp80) REVERT: F 205 LYS cc_start: 0.9478 (tppp) cc_final: 0.9144 (mttp) REVERT: F 349 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6889 (tm) REVERT: F 629 TYR cc_start: 0.7626 (m-80) cc_final: 0.7364 (m-80) REVERT: F 663 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.7874 (ttt) REVERT: F 927 MET cc_start: 0.8878 (mtp) cc_final: 0.8651 (mtm) REVERT: F 939 ASN cc_start: 0.8049 (m-40) cc_final: 0.7610 (p0) REVERT: F 963 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8362 (m) REVERT: F 1093 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.6075 (tt) REVERT: F 1186 TRP cc_start: 0.8127 (t60) cc_final: 0.7561 (t60) outliers start: 55 outliers final: 27 residues processed: 183 average time/residue: 0.5660 time to fit residues: 121.0972 Evaluate side-chains 161 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 663 MET Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1093 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 158 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 212 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1135 ASN ** F 70 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 = 0.3768 r_free = 0.3768 target = 0.082079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.057621 restraints weight = 70603.919| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.41 r_work: 0.3050 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25610 Z= 0.148 Angle : 0.549 14.157 34851 Z= 0.294 Chirality : 0.041 0.159 3837 Planarity : 0.004 0.045 4321 Dihedral : 14.023 165.630 3823 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.77 % Favored : 97.09 % Rotamer: Outliers : 1.91 % Allowed : 16.10 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.36 (0.16), residues: 2922 helix: 2.29 (0.14), residues: 1337 sheet: 0.08 (0.25), residues: 430 loop : -0.40 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1145 TYR 0.017 0.001 TYR F 788 PHE 0.025 0.001 PHE A 607 TRP 0.051 0.002 TRP A1098 HIS 0.007 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (25610) covalent geometry : angle 0.54908 / 0.29 (34851) hydrogen bonds : bond 0.03852 / 2.49 ( 1191) hydrogen bonds : angle 4.36775 / 3.06 ( 3367) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8752 (t0) cc_final: 0.8507 (t0) REVERT: A 205 LYS cc_start: 0.8622 (mtmp) cc_final: 0.8271 (mtmp) REVERT: A 208 LYS cc_start: 0.8639 (pttm) cc_final: 0.8390 (ptpp) REVERT: A 214 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8405 (tm) REVERT: A 397 GLU cc_start: -0.4396 (OUTLIER) cc_final: -0.5188 (pm20) REVERT: A 511 ARG cc_start: 0.8125 (pmm-80) cc_final: 0.7443 (tmm160) REVERT: A 939 ASN cc_start: 0.8247 (t0) cc_final: 0.7631 (p0) REVERT: A 1145 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7737 (ttm-80) REVERT: F 172 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9014 (mm) REVERT: F 177 ARG cc_start: 0.8596 (mmt-90) cc_final: 0.8111 (mmp80) REVERT: F 201 ASP cc_start: 0.8950 (t0) cc_final: 0.8693 (OUTLIER) REVERT: F 205 LYS cc_start: 0.9466 (tppp) cc_final: 0.9136 (mttp) REVERT: F 208 LYS cc_start: 0.8927 (tppt) cc_final: 0.8667 (tptt) REVERT: F 349 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6853 (tm) REVERT: F 629 TYR cc_start: 0.7668 (m-80) cc_final: 0.7403 (m-80) REVERT: F 663 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.7869 (ttt) REVERT: F 927 MET cc_start: 0.8883 (mtp) cc_final: 0.8650 (mtm) REVERT: F 939 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7562 (p0) REVERT: F 963 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8334 (m) REVERT: F 1093 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6120 (tt) REVERT: F 1186 TRP cc_start: 0.8142 (t60) cc_final: 0.7592 (t60) outliers start: 50 outliers final: 30 residues processed: 177 average time/residue: 0.5652 time to fit residues: 116.6098 Evaluate side-chains 170 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 663 MET Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1093 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 87 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1020 GLN A1135 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.081485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056796 restraints weight = 71029.218| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.44 r_work: 0.3025 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25610 Z= 0.221 Angle : 0.581 14.475 34851 Z= 0.309 Chirality : 0.043 0.161 3837 Planarity : 0.004 0.044 4321 Dihedral : 14.090 164.747 3823 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 1.83 % Allowed : 16.22 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.29 (0.16), residues: 2922 helix: 2.22 (0.14), residues: 1343 sheet: 0.05 (0.25), residues: 434 loop : -0.44 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1087 TYR 0.017 0.001 TYR F 788 PHE 0.029 0.002 PHE A 607 TRP 0.034 0.002 TRP A1098 HIS 0.009 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (25610) covalent geometry : angle 0.58071 / 0.31 (34851) hydrogen bonds : bond 0.04153 / 2.70 ( 1191) hydrogen bonds : angle 4.41822 / 3.09 ( 3367) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8775 (t0) cc_final: 0.8543 (t0) REVERT: A 205 LYS cc_start: 0.8644 (mtmp) cc_final: 0.8291 (mtmp) REVERT: A 208 LYS cc_start: 0.8655 (pttm) cc_final: 0.8412 (ptpp) REVERT: A 214 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8457 (tm) REVERT: A 397 GLU cc_start: -0.4324 (OUTLIER) cc_final: -0.5162 (pm20) REVERT: A 511 ARG cc_start: 0.8163 (pmm-80) cc_final: 0.7516 (tmm160) REVERT: A 939 ASN cc_start: 0.8243 (t0) cc_final: 0.7621 (p0) REVERT: F 177 ARG cc_start: 0.8600 (mmt-90) cc_final: 0.8123 (mmp80) REVERT: F 201 ASP cc_start: 0.8952 (t0) cc_final: 0.8693 (OUTLIER) REVERT: F 205 LYS cc_start: 0.9475 (tppp) cc_final: 0.9173 (mttp) REVERT: F 208 LYS cc_start: 0.8948 (tppt) cc_final: 0.8645 (tptt) REVERT: F 349 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6835 (tm) REVERT: F 629 TYR cc_start: 0.7719 (m-80) cc_final: 0.7412 (m-80) REVERT: F 927 MET cc_start: 0.8877 (mtp) cc_final: 0.8673 (mtm) REVERT: F 939 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7622 (p0) REVERT: F 963 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8274 (m) REVERT: F 1186 TRP cc_start: 0.8152 (t60) cc_final: 0.7597 (t60) outliers start: 48 outliers final: 31 residues processed: 178 average time/residue: 0.6483 time to fit residues: 134.4957 Evaluate side-chains 171 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 291 optimal weight: 7.9990 chunk 235 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1135 ASN ** F 70 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 = 0.3759 r_free = 0.3759 target = 0.081645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057041 restraints weight = 71137.503| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.42 r_work: 0.3032 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25610 Z= 0.199 Angle : 0.578 16.887 34851 Z= 0.307 Chirality : 0.042 0.163 3837 Planarity : 0.004 0.045 4321 Dihedral : 14.106 164.311 3823 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.94 % Favored : 96.92 % Rotamer: Outliers : 1.64 % Allowed : 16.67 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.30 (0.16), residues: 2922 helix: 2.25 (0.14), residues: 1337 sheet: 0.01 (0.25), residues: 434 loop : -0.44 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1145 TYR 0.016 0.001 TYR F 788 PHE 0.027 0.002 PHE A 607 TRP 0.032 0.002 TRP A1098 HIS 0.010 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (25610) covalent geometry : angle 0.57834 / 0.31 (34851) hydrogen bonds : bond 0.04043 / 2.63 ( 1191) hydrogen bonds : angle 4.39080 / 3.08 ( 3367) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8763 (t0) cc_final: 0.8531 (t0) REVERT: A 205 LYS cc_start: 0.8659 (mtmp) cc_final: 0.8355 (mtmp) REVERT: A 208 LYS cc_start: 0.8643 (pttm) cc_final: 0.8407 (ptpp) REVERT: A 214 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8465 (tm) REVERT: A 397 GLU cc_start: -0.4510 (OUTLIER) cc_final: -0.5244 (pm20) REVERT: A 511 ARG cc_start: 0.8169 (pmm-80) cc_final: 0.7536 (tmm160) REVERT: A 939 ASN cc_start: 0.8239 (t0) cc_final: 0.7631 (p0) REVERT: A 1130 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.6056 (mmtt) REVERT: A 1145 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7660 (ttm-80) REVERT: F 177 ARG cc_start: 0.8601 (mmt-90) cc_final: 0.8123 (mmp80) REVERT: F 201 ASP cc_start: 0.8980 (t0) cc_final: 0.8694 (t0) REVERT: F 205 LYS cc_start: 0.9463 (tppp) cc_final: 0.9167 (mttp) REVERT: F 208 LYS cc_start: 0.8959 (tppt) cc_final: 0.8656 (tptt) REVERT: F 349 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6806 (tm) REVERT: F 629 TYR cc_start: 0.7728 (m-80) cc_final: 0.7437 (m-80) REVERT: F 939 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7625 (p0) REVERT: F 963 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8280 (m) outliers start: 43 outliers final: 31 residues processed: 178 average time/residue: 0.6789 time to fit residues: 140.6080 Evaluate side-chains 172 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1130 LYS Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 145 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 288 optimal weight: 7.9990 chunk 224 optimal weight: 0.6980 chunk 289 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN ** F 70 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 = 0.3775 r_free = 0.3775 target = 0.082233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.057606 restraints weight = 70902.348| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.44 r_work: 0.3046 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25610 Z= 0.154 Angle : 0.562 15.771 34851 Z= 0.299 Chirality : 0.041 0.161 3837 Planarity : 0.004 0.050 4321 Dihedral : 14.053 164.425 3823 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.99 % Rotamer: Outliers : 1.68 % Allowed : 16.79 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.37 (0.16), residues: 2922 helix: 2.32 (0.14), residues: 1337 sheet: 0.06 (0.25), residues: 432 loop : -0.41 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1145 TYR 0.017 0.001 TYR F 788 PHE 0.025 0.001 PHE A 607 TRP 0.028 0.001 TRP A1098 HIS 0.007 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (25610) covalent geometry : angle 0.56152 / 0.30 (34851) hydrogen bonds : bond 0.03817 / 2.48 ( 1191) hydrogen bonds : angle 4.34757 / 3.04 ( 3367) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASN cc_start: 0.8796 (t0) cc_final: 0.8553 (t0) REVERT: A 205 LYS cc_start: 0.8653 (mtmp) cc_final: 0.8325 (mtmp) REVERT: A 208 LYS cc_start: 0.8650 (pttm) cc_final: 0.8413 (ptpp) REVERT: A 214 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8409 (tm) REVERT: A 397 GLU cc_start: -0.4464 (OUTLIER) cc_final: -0.5219 (pm20) REVERT: A 511 ARG cc_start: 0.8158 (pmm-80) cc_final: 0.7526 (tmm160) REVERT: A 939 ASN cc_start: 0.8240 (t0) cc_final: 0.7645 (p0) REVERT: A 1130 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6185 (mmtt) REVERT: A 1145 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7644 (ttm-80) REVERT: E 682 MET cc_start: 0.8609 (mtt) cc_final: 0.8327 (mtm) REVERT: F 177 ARG cc_start: 0.8584 (mmt-90) cc_final: 0.8106 (mmp80) REVERT: F 201 ASP cc_start: 0.9018 (t0) cc_final: 0.8664 (t0) REVERT: F 205 LYS cc_start: 0.9457 (tppp) cc_final: 0.9118 (mttp) REVERT: F 208 LYS cc_start: 0.8931 (tppt) cc_final: 0.8627 (tptt) REVERT: F 349 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6829 (tm) REVERT: F 629 TYR cc_start: 0.7700 (m-80) cc_final: 0.7408 (m-80) REVERT: F 939 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7606 (p0) REVERT: F 963 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8222 (m) REVERT: F 1093 ILE cc_start: 0.6385 (OUTLIER) cc_final: 0.6083 (tt) REVERT: F 1186 TRP cc_start: 0.8112 (t60) cc_final: 0.7546 (t60) outliers start: 44 outliers final: 28 residues processed: 176 average time/residue: 0.6475 time to fit residues: 132.4004 Evaluate side-chains 168 residues out of total 2621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1130 LYS Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 387 SER Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1093 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 178 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 262 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 93 optimal weight: 0.0020 chunk 111 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1135 ASN ** F 70 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 = 0.3784 r_free = 0.3784 target = 0.082626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.058090 restraints weight = 70768.772| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.44 r_work: 0.3061 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25610 Z= 0.127 Angle : 0.546 16.235 34851 Z= 0.291 Chirality : 0.040 0.160 3837 Planarity : 0.003 0.049 4321 Dihedral : 13.970 164.645 3821 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.99 % Rotamer: Outliers : 1.56 % Allowed : 17.05 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.47 (0.16), residues: 2922 helix: 2.40 (0.14), residues: 1337 sheet: 0.08 (0.25), residues: 433 loop : -0.36 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1087 TYR 0.015 0.001 TYR F 788 PHE 0.024 0.001 PHE A 607 TRP 0.029 0.001 TRP A1098 HIS 0.008 0.001 HIS E 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (25610) covalent geometry : angle 0.54575 / 0.29 (34851) hydrogen bonds : bond 0.03614 / 2.35 ( 1191) hydrogen bonds : angle 4.27356 / 2.99 ( 3367) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11485.98 seconds wall clock time: 195 minutes 37.41 seconds (11737.41 seconds total)