Starting phenix.real_space_refine on Sat Aug 8 03:36:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10mi_75286/08_2026/10mi_75286.cif Found real_map, /net/cci-nas-00/data/ceres_data/10mi_75286/08_2026/10mi_75286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10mi_75286/08_2026/10mi_75286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10mi_75286/08_2026/10mi_75286.map" model { file = "/net/cci-nas-00/data/ceres_data/10mi_75286/08_2026/10mi_75286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10mi_75286/08_2026/10mi_75286.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 73 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 14858 2.51 5 N 4281 2.21 5 O 5678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24981 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1720 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 221} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 645 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain: "P" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 665 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8485 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 61, 'TRANS': 1033} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 9981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9981 Classifications: {'peptide': 1278} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 60, 'TRANS': 1217} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "Q" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' MG': 2, ' ZN': 2, 'GTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "P" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 308 Classifications: {'water': 308} Link IDs: {None: 307} Chain: "D" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 367 Classifications: {'water': 367} Link IDs: {None: 366} Chain: "Q" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14014 SG CYS D 60 106.967 77.789 112.743 1.00 85.90 S ATOM 14032 SG CYS D 62 108.441 81.178 114.419 1.00 86.34 S ATOM 14141 SG CYS D 75 110.115 77.650 114.726 1.00 85.83 S ATOM 14167 SG CYS D 78 106.730 77.871 114.590 1.00 86.69 S ATOM 20582 SG CYS D 891 70.848 23.892 88.825 1.00 20.05 S ATOM 21149 SG CYS D 968 69.883 27.529 89.820 1.00 11.68 S ATOM 21191 SG CYS D 975 71.147 26.831 86.395 1.00 10.68 S ATOM 21209 SG CYS D 978 67.875 26.023 87.095 1.00 18.21 S Time building chain proxies: 5.24, per 1000 atoms: 0.21 Number of scatterers: 24981 At special positions: 0 Unit cell: (127.897, 133.826, 198.198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 87 16.00 P 73 15.00 Mg 2 11.99 O 5678 8.00 N 4281 7.00 C 14858 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: 1.68 Conformation dependent library (CDL) restraints added in 823.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 78 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 975 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 968 " Number of angles added : 12 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5358 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 41 sheets defined 39.6% alpha, 17.0% beta 31 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 203 through 220 Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.863A pdb=" N GLU A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 226 " --> pdb=" O ARG A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 226' Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.549A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.233A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.756A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 removed outlier: 3.709A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 60 " --> pdb=" O TYR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'C' and resid 54 through 65 removed outlier: 4.253A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 62 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 78 removed outlier: 3.523A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 removed outlier: 3.543A pdb=" N LEU C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 removed outlier: 3.629A pdb=" N LYS C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.755A pdb=" N GLU C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.901A pdb=" N LEU C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.906A pdb=" N THR C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 405 removed outlier: 3.698A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.687A pdb=" N GLY C 448 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.531A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.598A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 594' Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.711A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 856 through 858 No H-bonds generated for 'chain 'C' and resid 856 through 858' Processing helix chain 'C' and resid 920 through 925 removed outlier: 4.434A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 920 through 925' Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 990 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.693A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1107 removed outlier: 4.223A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.989A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.764A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 107 removed outlier: 3.579A pdb=" N PHE D 107 " --> pdb=" O ILE D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 107' Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 141 through 147 Processing helix chain 'D' and resid 147 through 187 Processing helix chain 'D' and resid 190 through 228 Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.652A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.600A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 300 removed outlier: 3.516A pdb=" N ALA D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.839A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.538A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.886A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 491 removed outlier: 4.096A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 675 Processing helix chain 'D' and resid 689 through 702 removed outlier: 3.540A pdb=" N GLU D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 705 through 726 removed outlier: 3.541A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.535A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 791 removed outlier: 3.784A pdb=" N GLU D 776 " --> pdb=" O GLU D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 removed outlier: 3.746A pdb=" N VAL D 803 " --> pdb=" O ILE D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 819 Processing helix chain 'D' and resid 845 through 866 Processing helix chain 'D' and resid 866 through 881 removed outlier: 3.614A pdb=" N SER D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 955 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.533A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1012 removed outlier: 3.836A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Proline residue: D1006 - end of helix removed outlier: 3.585A pdb=" N MET D1012 " --> pdb=" O THR D1008 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1017 removed outlier: 3.533A pdb=" N HIS D1016 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D1017 " --> pdb=" O THR D1014 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1013 through 1017' Processing helix chain 'D' and resid 1023 through 1036 removed outlier: 4.023A pdb=" N GLY D1027 " --> pdb=" O ASP D1023 " (cutoff:3.500A) Proline residue: D1029 - end of helix removed outlier: 3.559A pdb=" N GLU D1036 " --> pdb=" O GLN D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1125 removed outlier: 3.706A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1145 removed outlier: 3.776A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D1144 " --> pdb=" O GLU D1140 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1160 removed outlier: 3.989A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1196 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.506A pdb=" N SER D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.542A pdb=" N ILE D1238 " --> pdb=" O THR D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 15 removed outlier: 6.608A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 189 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.718A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.914A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 15 removed outlier: 6.377A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 99 removed outlier: 7.446A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.586A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'E' and resid 104 through 107 Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.625A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 5.450A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY C 155 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C 135 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N PHE C 153 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA C 137 " --> pdb=" O THR C 151 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR C 151 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE C 139 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER C 149 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASN C 141 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE C 147 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.498A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.600A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 213 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.379A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.694A pdb=" N GLU C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.597A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.881A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 676 through 677 Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.442A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LEU C 899 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU C 737 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.669A pdb=" N THR C 762 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 801 through 803 removed outlier: 3.876A pdb=" N VAL C 803 " --> pdb=" O LEU C 837 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD3, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.722A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD5, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.686A pdb=" N SER D 24 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N HIS D 94 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY D 26 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU D 96 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.742A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 328 through 329 removed outlier: 3.742A pdb=" N VAL D 328 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 633 through 637 Processing sheet with id=AD9, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 900 Processing sheet with id=AE2, first strand: chain 'D' and resid 902 through 904 Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 7.156A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1075 through 1077 removed outlier: 3.924A pdb=" N VAL D1075 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D1105 " --> pdb=" O GLY D1051 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.585A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 2.16 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: 6763 1.33 - 1.45: 3931 1.45 - 1.57: 13646 1.57 - 1.69: 141 1.69 - 1.81: 153 Bond restraints: 24634 Sorted by residual: bond pdb=" C3' DA Q 38 " pdb=" C2' DA Q 38 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" C3' DC P 41 " pdb=" C2' DC P 41 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DG P 12 " pdb=" C2' DG P 12 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.91e+00 bond pdb=" C3' DC P 32 " pdb=" C2' DC P 32 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.38e+00 bond pdb=" C3' DT P 16 " pdb=" C2' DT P 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.36e+00 ... (remaining 24629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 33140 2.03 - 4.06: 503 4.06 - 6.09: 37 6.09 - 8.12: 2 8.12 - 10.15: 4 Bond angle restraints: 33686 Sorted by residual: angle pdb=" C HIS D 653 " pdb=" CA HIS D 653 " pdb=" CB HIS D 653 " ideal model delta sigma weight residual 116.54 110.94 5.60 1.15e+00 7.56e-01 2.37e+01 angle pdb=" O4' DC P 27 " pdb=" C4' DC P 27 " pdb=" C3' DC P 27 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" O4' DC P 25 " pdb=" C4' DC P 25 " pdb=" C3' DC P 25 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.17e+01 angle pdb=" O4' DA P 26 " pdb=" C4' DA P 26 " pdb=" C3' DA P 26 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.11e+01 angle pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sigma weight residual 118.80 123.58 -4.78 1.10e+00 8.26e-01 1.89e+01 ... (remaining 33681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 14343 32.04 - 64.08: 527 64.08 - 96.11: 11 96.11 - 128.15: 2 128.15 - 160.19: 2 Dihedral angle restraints: 14885 sinusoidal: 6545 harmonic: 8340 Sorted by residual: dihedral pdb=" O4' C R 11 " pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sinusoidal sigma weight residual 200.00 40.42 159.58 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O2G GTP D1405 " pdb=" O3B GTP D1405 " pdb=" PG GTP D1405 " pdb=" PB GTP D1405 " ideal model delta sinusoidal sigma weight residual 177.30 17.11 160.19 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" CA VAL D 110 " pdb=" C VAL D 110 " pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta harmonic sigma weight residual 180.00 151.06 28.94 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 14882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3526 0.084 - 0.169: 316 0.169 - 0.253: 0 0.253 - 0.338: 0 0.338 - 0.422: 2 Chirality restraints: 3844 Sorted by residual: chirality pdb=" P G R 20 " pdb=" OP1 G R 20 " pdb=" OP2 G R 20 " pdb=" O5' G R 20 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" P DC P 25 " pdb=" OP1 DC P 25 " pdb=" OP2 DC P 25 " pdb=" O5' DC P 25 " both_signs ideal model delta sigma weight residual True 2.34 -2.71 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1' G R 20 " pdb=" O4' G R 20 " pdb=" C2' G R 20 " pdb=" N9 G R 20 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 3841 not shown) Planarity restraints: 4185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1028 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.36e+00 pdb=" N PRO D1029 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D1029 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D1029 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 571 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO C 572 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 572 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 572 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 110 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO D 111 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " -0.026 5.00e-02 4.00e+02 ... (remaining 4182 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 125 2.66 - 3.22: 21936 3.22 - 3.78: 36408 3.78 - 4.34: 53684 4.34 - 4.90: 87948 Nonbonded interactions: 200101 Sorted by model distance: nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D1404 " model vdw 2.101 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D1403 " model vdw 2.237 2.170 nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D1403 " model vdw 2.274 2.170 nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D1403 " model vdw 2.353 2.170 nonbonded pdb="MG MG D1404 " pdb=" O2G GTP D1405 " model vdw 2.429 2.170 ... (remaining 200096 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 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and (resid 1 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB )) or resid 25 through 226)) } 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: 5.370 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: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.600 Find NCS groups from input model: 0.200 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24642 Z= 0.230 Angle : 0.718 61.756 33698 Z= 0.398 Chirality : 0.046 0.422 3844 Planarity : 0.005 0.072 4185 Dihedral : 14.626 160.189 9527 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.79 % Allowed : 6.06 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 2904 helix: 0.53 (0.17), residues: 1017 sheet: 0.36 (0.26), residues: 395 loop : -1.05 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 473 TYR 0.015 0.001 TYR A 168 PHE 0.020 0.001 PHE D 6 TRP 0.010 0.001 TRP D 723 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.23 (24634) covalent geometry : angle 0.61024 / 0.39 (33686) hydrogen bonds : bond 0.16267 / 11.50 ( 1029) hydrogen bonds : angle 5.83465 / 4.11 ( 2820) metal coordination : bond 0.03846 / 1.99 ( 8) metal coordination : angle 20.06044 / 7.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 261 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 35 residues processed: 362 average time/residue: 0.6611 time to fit residues: 271.4003 Evaluate side-chains 172 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain C residue 99 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN B 200 ASN E 65 ASN E 100 HIS C 775 ASN C1066 GLN D 396 ASN D 505 HIS D 852 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.056609 restraints weight = 52973.382| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.13 r_work: 0.2600 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24642 Z= 0.154 Angle : 0.629 37.126 33698 Z= 0.315 Chirality : 0.043 0.198 3844 Planarity : 0.005 0.070 4185 Dihedral : 14.724 158.508 4046 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.48 % Allowed : 12.20 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 2904 helix: 0.97 (0.17), residues: 1020 sheet: 0.34 (0.24), residues: 449 loop : -0.81 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 667 TYR 0.015 0.001 TYR D 36 PHE 0.052 0.002 PHE D 6 TRP 0.007 0.001 TRP D 723 HIS 0.003 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (24634) covalent geometry : angle 0.58687 / 0.31 (33686) hydrogen bonds : bond 0.04980 / 3.46 ( 1029) hydrogen bonds : angle 4.61419 / 3.27 ( 2820) metal coordination : bond 0.01293 / 0.64 ( 8) metal coordination : angle 12.07585 / 4.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 148 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: B 95 MET cc_start: 0.9206 (mtm) cc_final: 0.8887 (mtp) REVERT: E 77 GLU cc_start: 0.7094 (pm20) cc_final: 0.6891 (pm20) REVERT: C 197 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8180 (ptmm) REVERT: C 505 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6748 (ptp-170) REVERT: C 672 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8030 (mmp) REVERT: C 835 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8167 (p) REVERT: C 962 GLU cc_start: 0.8518 (tp30) cc_final: 0.8203 (tp30) REVERT: D 36 TYR cc_start: 0.8236 (t80) cc_final: 0.7885 (t80) REVERT: D 37 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8570 (ttm110) REVERT: D 767 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6803 (t70) REVERT: D 810 ASN cc_start: 0.8688 (m110) cc_final: 0.8373 (m-40) outliers start: 85 outliers final: 42 residues processed: 219 average time/residue: 0.5371 time to fit residues: 138.2170 Evaluate side-chains 180 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 356 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 140 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 242 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN C 739 ASN C 875 GLN D 505 HIS D 852 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.056889 restraints weight = 53637.293| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.03 r_work: 0.2630 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24642 Z= 0.141 Angle : 0.546 19.303 33698 Z= 0.285 Chirality : 0.043 0.206 3844 Planarity : 0.004 0.052 4185 Dihedral : 14.606 159.160 4027 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.32 % Allowed : 12.53 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 2904 helix: 1.28 (0.17), residues: 1030 sheet: 0.37 (0.25), residues: 431 loop : -0.76 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 279 TYR 0.012 0.001 TYR C 278 PHE 0.034 0.001 PHE D 6 TRP 0.008 0.001 TRP C 938 HIS 0.003 0.001 HIS D 854 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (24634) covalent geometry : angle 0.53122 / 0.28 (33686) hydrogen bonds : bond 0.04488 / 3.11 ( 1029) hydrogen bonds : angle 4.32142 / 3.06 ( 2820) metal coordination : bond 0.01032 / 0.51 ( 8) metal coordination : angle 6.59311 / 2.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 147 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: C 505 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.6899 (ptp-170) REVERT: C 563 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8379 (mtp180) REVERT: C 672 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.7940 (mmp) REVERT: C 835 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8245 (p) REVERT: C 962 GLU cc_start: 0.8382 (tp30) cc_final: 0.8034 (tp30) REVERT: D 36 TYR cc_start: 0.8283 (t80) cc_final: 0.7965 (t80) REVERT: D 37 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8569 (ttm110) REVERT: D 767 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6699 (t70) REVERT: D 810 ASN cc_start: 0.8729 (m110) cc_final: 0.8479 (m-40) REVERT: D 1112 MET cc_start: 0.7805 (mmp) cc_final: 0.7456 (mmp) outliers start: 81 outliers final: 34 residues processed: 215 average time/residue: 0.5170 time to fit residues: 131.4564 Evaluate side-chains 171 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 767 HIS Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 279 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 62 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 287 optimal weight: 6.9990 chunk 291 optimal weight: 0.0470 chunk 210 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 889 HIS D 207 GLN D 341 ASN D 505 HIS D 693 GLN D 852 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.053507 restraints weight = 52906.958| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.08 r_work: 0.2532 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24642 Z= 0.225 Angle : 0.589 13.639 33698 Z= 0.310 Chirality : 0.045 0.159 3844 Planarity : 0.004 0.049 4185 Dihedral : 14.667 158.217 4023 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.44 % Allowed : 13.14 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 2904 helix: 1.37 (0.17), residues: 1035 sheet: 0.24 (0.24), residues: 452 loop : -0.79 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 279 TYR 0.018 0.001 TYR D 251 PHE 0.018 0.002 PHE D 7 TRP 0.008 0.001 TRP C 70 HIS 0.005 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (24634) covalent geometry : angle 0.58133 / 0.31 (33686) hydrogen bonds : bond 0.05359 / 3.70 ( 1029) hydrogen bonds : angle 4.28258 / 3.03 ( 2820) metal coordination : bond 0.01208 / 0.59 ( 8) metal coordination : angle 5.04106 / 2.07 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 137 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8585 (ttm-80) REVERT: B 177 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8476 (OUTLIER) REVERT: C 433 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8695 (p) REVERT: C 505 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.6984 (ptp-170) REVERT: C 563 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8419 (mtp180) REVERT: C 672 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.7979 (mmp) REVERT: C 835 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8290 (p) REVERT: C 962 GLU cc_start: 0.8552 (tp30) cc_final: 0.8210 (tp30) REVERT: D 36 TYR cc_start: 0.8412 (t80) cc_final: 0.8041 (t80) REVERT: D 37 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8607 (ttm110) REVERT: D 60 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7417 (t) REVERT: D 1112 MET cc_start: 0.7911 (mmp) cc_final: 0.7648 (mmp) outliers start: 84 outliers final: 34 residues processed: 207 average time/residue: 0.5343 time to fit residues: 129.2324 Evaluate side-chains 172 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 873 VAL Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 270 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 852 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.053636 restraints weight = 53039.157| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.10 r_work: 0.2540 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24642 Z= 0.187 Angle : 0.553 10.200 33698 Z= 0.293 Chirality : 0.044 0.171 3844 Planarity : 0.004 0.050 4185 Dihedral : 14.640 159.164 4017 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.07 % Allowed : 14.04 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2904 helix: 1.45 (0.17), residues: 1038 sheet: 0.33 (0.25), residues: 428 loop : -0.79 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 620 TYR 0.015 0.001 TYR A 168 PHE 0.014 0.001 PHE D 7 TRP 0.008 0.001 TRP C 70 HIS 0.003 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (24634) covalent geometry : angle 0.54710 / 0.29 (33686) hydrogen bonds : bond 0.04842 / 3.35 ( 1029) hydrogen bonds : angle 4.22498 / 2.99 ( 2820) metal coordination : bond 0.00974 / 0.47 ( 8) metal coordination : angle 4.21871 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 139 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8534 (ttm-80) REVERT: B 177 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8445 (ttmm) REVERT: B 185 GLN cc_start: 0.4778 (tt0) cc_final: 0.4519 (mt0) REVERT: C 274 LEU cc_start: 0.8947 (mt) cc_final: 0.8718 (tp) REVERT: C 429 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8421 (tm-30) REVERT: C 433 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8588 (p) REVERT: C 505 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7004 (ptp-170) REVERT: C 563 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8417 (mtp180) REVERT: C 672 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.7972 (mmp) REVERT: C 835 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8306 (p) REVERT: C 962 GLU cc_start: 0.8550 (tp30) cc_final: 0.8176 (tp30) REVERT: D 36 TYR cc_start: 0.8431 (t80) cc_final: 0.8061 (t80) REVERT: D 37 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8643 (ttm110) REVERT: D 145 HIS cc_start: 0.9322 (OUTLIER) cc_final: 0.9101 (p90) outliers start: 75 outliers final: 37 residues processed: 198 average time/residue: 0.5225 time to fit residues: 120.9620 Evaluate side-chains 176 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 687 CYS Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 232 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 294 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 33 optimal weight: 0.0570 chunk 243 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 177 optimal weight: 0.0470 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN E 70 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 852 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.054858 restraints weight = 52992.262| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.09 r_work: 0.2570 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24642 Z= 0.122 Angle : 0.521 9.340 33698 Z= 0.276 Chirality : 0.042 0.218 3844 Planarity : 0.004 0.051 4185 Dihedral : 14.596 159.918 4017 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.29 % Allowed : 15.10 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2904 helix: 1.62 (0.17), residues: 1040 sheet: 0.39 (0.26), residues: 417 loop : -0.69 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 67 TYR 0.011 0.001 TYR C 344 PHE 0.018 0.001 PHE C 99 TRP 0.008 0.001 TRP C 938 HIS 0.003 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (24634) covalent geometry : angle 0.51777 / 0.28 (33686) hydrogen bonds : bond 0.04069 / 2.81 ( 1029) hydrogen bonds : angle 4.09879 / 2.90 ( 2820) metal coordination : bond 0.00588 / 0.28 ( 8) metal coordination : angle 3.26942 / 1.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 139 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASN cc_start: 0.9492 (t0) cc_final: 0.9218 (t0) REVERT: B 177 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8349 (ttmm) REVERT: E 70 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6393 (tm-30) REVERT: C 429 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8450 (tm-30) REVERT: C 433 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8574 (p) REVERT: C 505 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.6956 (ptp-170) REVERT: C 563 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8398 (mtp180) REVERT: C 835 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8302 (p) REVERT: C 962 GLU cc_start: 0.8532 (tp30) cc_final: 0.8144 (tp30) REVERT: D 36 TYR cc_start: 0.8474 (t80) cc_final: 0.8099 (t80) REVERT: D 37 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8622 (ttm110) REVERT: D 145 HIS cc_start: 0.9334 (OUTLIER) cc_final: 0.9124 (p90) REVERT: D 1112 MET cc_start: 0.8024 (mmp) cc_final: 0.7722 (mmp) outliers start: 56 outliers final: 27 residues processed: 184 average time/residue: 0.5300 time to fit residues: 114.2580 Evaluate side-chains 164 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1111 ASN Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 268 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 169 optimal weight: 0.4980 chunk 218 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 49 optimal weight: 0.0030 chunk 173 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 852 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.089225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.055575 restraints weight = 52854.664| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.10 r_work: 0.2559 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24642 Z= 0.105 Angle : 0.506 11.315 33698 Z= 0.266 Chirality : 0.041 0.213 3844 Planarity : 0.004 0.059 4185 Dihedral : 14.536 159.741 4014 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.25 % Allowed : 15.47 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2904 helix: 1.69 (0.17), residues: 1048 sheet: 0.51 (0.26), residues: 408 loop : -0.65 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1085 TYR 0.010 0.001 TYR C 344 PHE 0.015 0.001 PHE D 6 TRP 0.009 0.001 TRP C 938 HIS 0.004 0.000 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (24634) covalent geometry : angle 0.50332 / 0.27 (33686) hydrogen bonds : bond 0.03715 / 2.56 ( 1029) hydrogen bonds : angle 4.00132 / 2.84 ( 2820) metal coordination : bond 0.00429 / 0.21 ( 8) metal coordination : angle 2.83968 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8172 (ptpp) REVERT: A 200 ASN cc_start: 0.9465 (t0) cc_final: 0.9176 (t0) REVERT: B 152 ASN cc_start: 0.7366 (t0) cc_final: 0.7053 (p0) REVERT: B 177 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8310 (ttmm) REVERT: C 429 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 433 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8495 (p) REVERT: C 505 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.6834 (ptp-170) REVERT: C 563 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8343 (mtp180) REVERT: C 835 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8254 (p) REVERT: C 843 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: C 962 GLU cc_start: 0.8527 (tp30) cc_final: 0.8093 (tp30) REVERT: D 36 TYR cc_start: 0.8505 (t80) cc_final: 0.8126 (t80) REVERT: D 37 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8592 (ttm110) REVERT: D 145 HIS cc_start: 0.9385 (OUTLIER) cc_final: 0.9176 (p90) REVERT: D 1112 MET cc_start: 0.7895 (mmp) cc_final: 0.7662 (mmp) outliers start: 55 outliers final: 28 residues processed: 183 average time/residue: 0.5428 time to fit residues: 115.9182 Evaluate side-chains 171 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain C residue 1111 ASN Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 230 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 283 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN E 70 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN D 852 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.055293 restraints weight = 52871.159| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.10 r_work: 0.2583 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24642 Z= 0.118 Angle : 0.505 9.141 33698 Z= 0.266 Chirality : 0.042 0.248 3844 Planarity : 0.004 0.049 4185 Dihedral : 14.514 159.268 4011 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.09 % Allowed : 15.80 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2904 helix: 1.74 (0.17), residues: 1048 sheet: 0.57 (0.26), residues: 408 loop : -0.63 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 67 TYR 0.010 0.001 TYR A 168 PHE 0.015 0.001 PHE D 6 TRP 0.008 0.001 TRP C 938 HIS 0.004 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (24634) covalent geometry : angle 0.50254 / 0.27 (33686) hydrogen bonds : bond 0.03801 / 2.61 ( 1029) hydrogen bonds : angle 3.96533 / 2.82 ( 2820) metal coordination : bond 0.00506 / 0.24 ( 8) metal coordination : angle 2.69169 / 1.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8280 (ptpp) REVERT: A 200 ASN cc_start: 0.9482 (t0) cc_final: 0.9203 (t0) REVERT: B 152 ASN cc_start: 0.7428 (t0) cc_final: 0.7097 (p0) REVERT: B 177 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8389 (ttmm) REVERT: E 70 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: C 429 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 433 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8585 (p) REVERT: C 505 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.6973 (ptp-170) REVERT: C 563 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8387 (mtp180) REVERT: C 835 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8327 (p) REVERT: C 843 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: C 962 GLU cc_start: 0.8496 (tp30) cc_final: 0.8092 (tp30) REVERT: D 36 TYR cc_start: 0.8515 (t80) cc_final: 0.8151 (t80) REVERT: D 37 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8656 (ttm110) outliers start: 51 outliers final: 29 residues processed: 178 average time/residue: 0.5710 time to fit residues: 118.3182 Evaluate side-chains 172 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1217 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 157 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 205 optimal weight: 0.0010 chunk 273 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.055356 restraints weight = 53266.180| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.11 r_work: 0.2585 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24642 Z= 0.114 Angle : 0.502 8.672 33698 Z= 0.264 Chirality : 0.042 0.264 3844 Planarity : 0.004 0.049 4185 Dihedral : 14.508 158.970 4011 Min Nonbonded Distance : 1.530 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.96 % Allowed : 16.05 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 2904 helix: 1.78 (0.17), residues: 1047 sheet: 0.56 (0.26), residues: 409 loop : -0.60 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1085 TYR 0.010 0.001 TYR C 344 PHE 0.016 0.001 PHE D 6 TRP 0.008 0.001 TRP C 938 HIS 0.005 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (24634) covalent geometry : angle 0.50004 / 0.26 (33686) hydrogen bonds : bond 0.03737 / 2.57 ( 1029) hydrogen bonds : angle 3.94247 / 2.80 ( 2820) metal coordination : bond 0.00460 / 0.22 ( 8) metal coordination : angle 2.54011 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8253 (ptpp) REVERT: A 200 ASN cc_start: 0.9480 (t0) cc_final: 0.9208 (t0) REVERT: B 152 ASN cc_start: 0.7447 (t0) cc_final: 0.7115 (p0) REVERT: B 177 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8397 (ttmm) REVERT: C 429 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8465 (tm-30) REVERT: C 433 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8582 (p) REVERT: C 505 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.6971 (ptp-170) REVERT: C 563 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8388 (mtp180) REVERT: C 835 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8350 (p) REVERT: C 843 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: C 962 GLU cc_start: 0.8499 (tp30) cc_final: 0.8091 (tp30) REVERT: D 36 TYR cc_start: 0.8518 (t80) cc_final: 0.8151 (t80) REVERT: D 37 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8665 (ttm110) REVERT: D 145 HIS cc_start: 0.9401 (OUTLIER) cc_final: 0.9178 (p90) REVERT: D 1112 MET cc_start: 0.7872 (mmp) cc_final: 0.7640 (mmp) outliers start: 48 outliers final: 33 residues processed: 178 average time/residue: 0.5573 time to fit residues: 115.4551 Evaluate side-chains 174 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain C residue 571 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 37 ARG Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1173 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 119 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 293 optimal weight: 40.0000 chunk 27 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.4341 > 50:) chunk 103 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 852 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.087705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.054023 restraints weight = 53434.793| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.11 r_work: 0.2553 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24642 Z= 0.181 Angle : 0.538 9.335 33698 Z= 0.282 Chirality : 0.043 0.230 3844 Planarity : 0.004 0.049 4185 Dihedral : 14.525 158.596 4010 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.84 % Allowed : 16.05 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2904 helix: 1.75 (0.17), residues: 1041 sheet: 0.50 (0.26), residues: 409 loop : -0.63 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 67 TYR 0.014 0.001 TYR A 168 PHE 0.016 0.001 PHE D 6 TRP 0.006 0.001 TRP C 938 HIS 0.004 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (24634) covalent geometry : angle 0.53562 / 0.28 (33686) hydrogen bonds : bond 0.04366 / 2.99 ( 1029) hydrogen bonds : angle 4.00613 / 2.84 ( 2820) metal coordination : bond 0.00780 / 0.38 ( 8) metal coordination : angle 2.79394 / 1.33 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8309 (ptpp) REVERT: B 152 ASN cc_start: 0.7477 (t0) cc_final: 0.7160 (p0) REVERT: B 177 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8434 (ttmm) REVERT: E 77 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: C 274 LEU cc_start: 0.8959 (mt) cc_final: 0.8659 (tp) REVERT: C 429 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8471 (tm-30) REVERT: C 433 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8602 (p) REVERT: C 505 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6990 (ptp-170) REVERT: C 563 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8406 (mtp180) REVERT: C 835 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8387 (p) REVERT: C 843 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: C 962 GLU cc_start: 0.8517 (tp30) cc_final: 0.8113 (tp30) REVERT: D 36 TYR cc_start: 0.8539 (t80) cc_final: 0.8177 (t80) REVERT: D 1112 MET cc_start: 0.7956 (mmp) cc_final: 0.7707 (mmp) outliers start: 45 outliers final: 31 residues processed: 173 average time/residue: 0.5950 time to fit residues: 120.4424 Evaluate side-chains 174 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 843 GLU Chi-restraints excluded: chain C residue 1051 MET Chi-restraints excluded: chain C residue 1062 GLN Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1173 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 6 optimal weight: 0.6980 chunk 207 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 228 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 143 optimal weight: 0.0670 chunk 290 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 119 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D 852 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.089031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.055428 restraints weight = 52980.453| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.11 r_work: 0.2587 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24642 Z= 0.102 Angle : 0.507 8.536 33698 Z= 0.266 Chirality : 0.041 0.237 3844 Planarity : 0.004 0.051 4185 Dihedral : 14.514 158.770 4010 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.68 % Allowed : 16.37 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 2904 helix: 1.83 (0.17), residues: 1046 sheet: 0.56 (0.26), residues: 409 loop : -0.59 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D1052 TYR 0.010 0.001 TYR C 344 PHE 0.016 0.001 PHE D 6 TRP 0.010 0.001 TRP C 938 HIS 0.007 0.001 HIS D 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (24634) covalent geometry : angle 0.50516 / 0.27 (33686) hydrogen bonds : bond 0.03681 / 2.53 ( 1029) hydrogen bonds : angle 3.93861 / 2.80 ( 2820) metal coordination : bond 0.00334 / 0.15 ( 8) metal coordination : angle 2.44685 / 1.18 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6174.85 seconds wall clock time: 105 minutes 45.08 seconds (6345.08 seconds total)