Starting phenix.real_space_refine on Sat Sep 12 22:32:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ifr_9656/09_2026/6ifr_9656.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ifr_9656/09_2026/6ifr_9656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ifr_9656/09_2026/6ifr_9656.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ifr_9656/09_2026/6ifr_9656.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ifr_9656/09_2026/6ifr_9656.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ifr_9656/09_2026/6ifr_9656.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ifr_9656/09_2026/6ifr_9656.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ifr_9656/09_2026/6ifr_9656.map" } resolution = 3.4 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 76 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 12006 2.51 5 N 3256 2.21 5 O 3843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19219 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5549 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 685} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1610 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2289 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2832 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 18, 'TRANS': 334} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'RNAv2': 35} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 18} Chain: "J" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 752 Classifications: {'RNAv2': 35} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 4, 'rna3p': 30} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.77, per 1000 atoms: 0.20 Number of scatterers: 19219 At special positions: 0 Unit cell: (92.56, 135.2, 170.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 76 15.00 Mg 2 11.99 O 3843 8.00 N 3256 7.00 C 12006 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 672.9 milliseconds 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 22 sheets defined 37.6% alpha, 11.0% beta 22 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 removed outlier: 3.653A pdb=" N ASP A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.516A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.615A pdb=" N VAL A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.721A pdb=" N SER A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 removed outlier: 3.610A pdb=" N ASN A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 removed outlier: 4.086A pdb=" N ARG A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.763A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.963A pdb=" N TYR A 236 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.245A pdb=" N ILE A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 4.062A pdb=" N ALA A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.669A pdb=" N VAL A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.739A pdb=" N ILE A 353 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 378 removed outlier: 3.554A pdb=" N VAL A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 421 through 430 removed outlier: 4.888A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A 427 " --> pdb=" O ARG A 423 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 removed outlier: 3.536A pdb=" N TYR A 498 " --> pdb=" O ILE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 removed outlier: 4.350A pdb=" N LYS A 503 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 541 through 557 removed outlier: 3.688A pdb=" N PHE A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 564 removed outlier: 4.174A pdb=" N GLN A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 604 removed outlier: 3.664A pdb=" N ILE A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.569A pdb=" N HIS A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 662 removed outlier: 3.566A pdb=" N THR A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 removed outlier: 3.626A pdb=" N GLN A 669 " --> pdb=" O ASP A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.606A pdb=" N ASN A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 removed outlier: 3.786A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 734 removed outlier: 3.870A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 754 removed outlier: 3.662A pdb=" N GLU A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 36 through 48 removed outlier: 3.720A pdb=" N ASN D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.907A pdb=" N LYS D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 79 removed outlier: 3.772A pdb=" N ILE D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 77 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG D 79 " --> pdb=" O TYR D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 90 removed outlier: 3.631A pdb=" N LYS D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.670A pdb=" N ARG D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 113 " --> pdb=" O CYS D 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 36 through 48 removed outlier: 3.722A pdb=" N ASN C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 55 removed outlier: 3.906A pdb=" N LYS C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 79 removed outlier: 3.772A pdb=" N ILE C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 90 removed outlier: 3.631A pdb=" N LYS C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.671A pdb=" N ARG C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 113 " --> pdb=" O CYS C 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 61 removed outlier: 3.503A pdb=" N LYS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 75 removed outlier: 3.533A pdb=" N ASP G 75 " --> pdb=" O PRO G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 84 Processing helix chain 'G' and resid 128 through 132 removed outlier: 3.772A pdb=" N ALA G 131 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU G 132 " --> pdb=" O ILE G 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 128 through 132' Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 164 through 177 removed outlier: 4.019A pdb=" N LYS G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 177 " --> pdb=" O GLY G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 214 removed outlier: 3.957A pdb=" N GLU G 214 " --> pdb=" O LYS G 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.801A pdb=" N LYS F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 62 " --> pdb=" O THR F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 removed outlier: 3.524A pdb=" N ASP F 75 " --> pdb=" O PRO F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 110 Processing helix chain 'F' and resid 162 through 177 removed outlier: 3.565A pdb=" N PHE F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.537A pdb=" N GLY F 189 " --> pdb=" O GLY F 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 removed outlier: 3.539A pdb=" N LYS E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 Processing helix chain 'E' and resid 105 through 110 removed outlier: 4.272A pdb=" N ASP E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 168 removed outlier: 3.523A pdb=" N PHE E 167 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS E 168 " --> pdb=" O GLU E 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 164 through 168' Processing helix chain 'E' and resid 169 through 179 removed outlier: 3.617A pdb=" N LEU E 179 " --> pdb=" O LYS E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 214 Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.684A pdb=" N ILE B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.656A pdb=" N GLU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.809A pdb=" N SER B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 221 through 228 removed outlier: 4.087A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 53 Processing helix chain 'H' and resid 55 through 63 Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'H' and resid 74 through 81 removed outlier: 4.038A pdb=" N PHE H 78 " --> pdb=" O ARG H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 removed outlier: 3.614A pdb=" N GLY H 134 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 182 Processing helix chain 'H' and resid 193 through 197 removed outlier: 3.721A pdb=" N SER H 196 " --> pdb=" O ASP H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 245 removed outlier: 3.554A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE H 243 " --> pdb=" O ALA H 239 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU H 244 " --> pdb=" O GLY H 240 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU H 245 " --> pdb=" O ARG H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 259 removed outlier: 4.007A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA H 252 " --> pdb=" O LYS H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 300 removed outlier: 3.962A pdb=" N GLN H 300 " --> pdb=" O ASP H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 304 removed outlier: 3.786A pdb=" N SER H 304 " --> pdb=" O ARG H 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 301 through 304' Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 307 removed outlier: 3.515A pdb=" N ALA A 306 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.526A pdb=" N TYR A 340 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 454 through 456 removed outlier: 3.698A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 483 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 574 Processing sheet with id=AA5, first strand: chain 'G' and resid 96 through 99 removed outlier: 3.821A pdb=" N ARG G 99 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU G 150 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 96 through 99 removed outlier: 3.821A pdb=" N ARG G 99 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU G 150 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS G 5 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 118 through 122 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 3.907A pdb=" N PHE F 102 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.725A pdb=" N LYS F 5 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN F 11 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASN F 197 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARG F 13 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE F 195 " --> pdb=" O ARG F 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 118 through 122 Processing sheet with id=AB2, first strand: chain 'F' and resid 125 through 126 Processing sheet with id=AB3, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.630A pdb=" N ILE E 152 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS E 5 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149 Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 123 Processing sheet with id=AB6, first strand: chain 'B' and resid 5 through 8 Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AB8, first strand: chain 'B' and resid 129 through 134 Processing sheet with id=AB9, first strand: chain 'B' and resid 204 through 205 removed outlier: 3.621A pdb=" N THR B 205 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 184 through 186 removed outlier: 3.858A pdb=" N THR H 226 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'H' and resid 37 through 39 Processing sheet with id=AC4, first strand: chain 'H' and resid 213 through 214 552 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.72 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: 4020 1.33 - 1.45: 4869 1.45 - 1.57: 10621 1.57 - 1.69: 149 1.69 - 1.81: 67 Bond restraints: 19726 Sorted by residual: bond pdb=" C4 ATP A 802 " pdb=" C5 ATP A 802 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.00e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.58e+01 bond pdb=" C5 ATP A 802 " pdb=" C6 ATP A 802 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.57e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.47e+01 bond pdb=" C4 ATP A 802 " pdb=" N9 ATP A 802 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.17e+01 ... (remaining 19721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 26566 4.12 - 8.25: 320 8.25 - 12.37: 44 12.37 - 16.50: 8 16.50 - 20.62: 3 Bond angle restraints: 26941 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 119.25 20.62 1.00e+00 1.00e+00 4.25e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 120.03 16.80 1.00e+00 1.00e+00 2.82e+02 angle pdb=" PB ATP A 802 " pdb=" O3B ATP A 802 " pdb=" PG ATP A 802 " ideal model delta sigma weight residual 139.87 123.95 15.92 1.00e+00 1.00e+00 2.54e+02 angle pdb=" PA ATP A 802 " pdb=" O3A ATP A 802 " pdb=" PB ATP A 802 " ideal model delta sigma weight residual 136.83 123.83 13.00 1.00e+00 1.00e+00 1.69e+02 angle pdb=" N GLY G 186 " pdb=" CA GLY G 186 " pdb=" C GLY G 186 " ideal model delta sigma weight residual 112.73 126.68 -13.95 1.20e+00 6.94e-01 1.35e+02 ... (remaining 26936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.08: 11145 27.08 - 54.16: 453 54.16 - 81.24: 88 81.24 - 108.32: 0 108.32 - 135.40: 1 Dihedral angle restraints: 11687 sinusoidal: 5204 harmonic: 6483 Sorted by residual: dihedral pdb=" C4' A N 26 " pdb=" C3' A N 26 " pdb=" C2' A N 26 " pdb=" C1' A N 26 " ideal model delta sinusoidal sigma weight residual 36.34 -40.02 76.37 1 3.10e+00 1.04e-01 7.64e+02 dihedral pdb=" C4' C N 2 " pdb=" C3' C N 2 " pdb=" C2' C N 2 " pdb=" C1' C N 2 " ideal model delta sinusoidal sigma weight residual 36.34 -37.41 73.75 1 3.10e+00 1.04e-01 7.20e+02 dihedral pdb=" C4' G N 3 " pdb=" C3' G N 3 " pdb=" C2' G N 3 " pdb=" C1' G N 3 " ideal model delta sinusoidal sigma weight residual 36.34 -37.20 73.54 1 3.10e+00 1.04e-01 7.16e+02 ... (remaining 11684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2589 0.091 - 0.181: 306 0.181 - 0.272: 109 0.272 - 0.362: 34 0.362 - 0.453: 4 Chirality restraints: 3042 Sorted by residual: chirality pdb=" CA GLN G 162 " pdb=" N GLN G 162 " pdb=" C GLN G 162 " pdb=" CB GLN G 162 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CA TYR A 224 " pdb=" N TYR A 224 " pdb=" C TYR A 224 " pdb=" CB TYR A 224 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C3' A J 20 " pdb=" C4' A J 20 " pdb=" O3' A J 20 " pdb=" C2' A J 20 " both_signs ideal model delta sigma weight residual False -2.50 -2.09 -0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 3039 not shown) Planarity restraints: 3196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 221 " -0.022 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C ARG A 221 " 0.080 2.00e-02 2.50e+03 pdb=" O ARG A 221 " -0.031 2.00e-02 2.50e+03 pdb=" N HIS A 222 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP A 802 " -0.013 2.00e-02 2.50e+03 2.46e-02 1.67e+01 pdb=" C2 ATP A 802 " 0.006 2.00e-02 2.50e+03 pdb=" C4 ATP A 802 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ATP A 802 " 0.031 2.00e-02 2.50e+03 pdb=" C6 ATP A 802 " -0.069 2.00e-02 2.50e+03 pdb=" C8 ATP A 802 " -0.005 2.00e-02 2.50e+03 pdb=" N1 ATP A 802 " 0.022 2.00e-02 2.50e+03 pdb=" N3 ATP A 802 " -0.001 2.00e-02 2.50e+03 pdb=" N6 ATP A 802 " 0.010 2.00e-02 2.50e+03 pdb=" N7 ATP A 802 " 0.012 2.00e-02 2.50e+03 pdb=" N9 ATP A 802 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.030 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP A 732 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.006 2.00e-02 2.50e+03 ... (remaining 3193 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 17 2.23 - 2.89: 7363 2.89 - 3.56: 27070 3.56 - 4.23: 48040 4.23 - 4.90: 79135 Nonbonded interactions: 161625 Sorted by model distance: nonbonded pdb=" OG SER G 187 " pdb=" NZ LYS H 133 " model vdw 1.558 3.120 nonbonded pdb=" NH1 ARG G 81 " pdb=" OE1 GLN G 162 " model vdw 1.600 3.120 nonbonded pdb=" N GLN H 294 " pdb=" OE1 GLN H 294 " model vdw 2.076 3.120 nonbonded pdb=" N ASP E 39 " pdb=" OD1 ASP E 39 " model vdw 2.082 3.120 nonbonded pdb=" O2A ATP A 802 " pdb="MG MG A 804 " model vdw 2.099 2.170 ... (remaining 161620 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 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 2 through 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB )) or resid 94 through 156 or (resid 157 through 158 and ( \ name N or name CA or name C or name O or name CB )) or resid 159 through 217)) selection = (chain 'F' and (resid 2 through 65 or resid 77 through 217)) selection = (chain 'G' and (resid 2 through 65 or resid 77 through 92 or (resid 93 and (name \ N or name CA or name C or name O or name CB )) or resid 94 through 157 or (resi \ d 158 and (name N or name CA or name C or name O or name CB )) or resid 159 or ( \ resid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 \ through 217)) } 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.140 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.007 0.077 19727 Z= 0.336 Angle : 1.204 20.620 26941 Z= 0.666 Chirality : 0.077 0.453 3042 Planarity : 0.006 0.056 3196 Dihedral : 14.205 135.402 7505 Min Nonbonded Distance : 1.558 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.02 % Favored : 87.66 % Rotamer: Outliers : 1.13 % Allowed : 7.62 % Favored : 91.26 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -5.42 (0.13), residues: 2188 helix: -4.31 (0.08), residues: 737 sheet: -3.00 (0.26), residues: 322 loop : -3.27 (0.15), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 41 TYR 0.040 0.003 TYR A 300 PHE 0.042 0.003 PHE A 241 TRP 0.062 0.005 TRP A 732 HIS 0.008 0.002 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.34 (19726) covalent geometry : angle 1.20425 / 0.67 (26941) hydrogen bonds : bond 0.27809 / 18.07 ( 583) hydrogen bonds : angle 10.57267 / 7.39 ( 1644) Misc. bond : bond 0.01946 / 1.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 575 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 VAL cc_start: 0.7351 (m) cc_final: 0.7078 (m) REVERT: A 198 LEU cc_start: 0.8706 (tm) cc_final: 0.8454 (tp) REVERT: A 222 HIS cc_start: 0.6739 (p90) cc_final: 0.6332 (m-70) REVERT: A 434 HIS cc_start: 0.7056 (m-70) cc_final: 0.6477 (m90) REVERT: A 447 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8593 (tt) REVERT: G 103 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6236 (tt) REVERT: G 154 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7086 (tt0) REVERT: F 119 GLU cc_start: 0.7960 (pp20) cc_final: 0.7623 (pp20) REVERT: F 206 ASN cc_start: 0.7376 (m-40) cc_final: 0.6456 (m-40) REVERT: E 117 TYR cc_start: 0.8333 (m-80) cc_final: 0.8024 (m-80) REVERT: E 168 LYS cc_start: 0.7902 (mtmp) cc_final: 0.7659 (ptpp) REVERT: B 219 LEU cc_start: 0.8613 (tm) cc_final: 0.8369 (tp) outliers start: 21 outliers final: 4 residues processed: 590 average time/residue: 0.1605 time to fit residues: 136.4815 Evaluate side-chains 276 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 270 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 223 ASN A 252 GLN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 434 HIS A 436 HIS A 497 ASN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 676 HIS D 76 GLN C 76 GLN C 106 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 144 ASN E 159 ASN E 161 ASN B 125 HIS B 134 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 249 ASN B 255 GLN B 288 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106777 restraints weight = 37037.650| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.09 r_work: 0.3317 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19727 Z= 0.165 Angle : 0.935 14.912 26941 Z= 0.435 Chirality : 0.080 1.524 3042 Planarity : 0.005 0.080 3196 Dihedral : 12.380 157.062 3269 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.65 % Favored : 89.26 % Rotamer: Outliers : 3.22 % Allowed : 13.41 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.32 (0.15), residues: 2188 helix: -2.81 (0.14), residues: 748 sheet: -2.63 (0.28), residues: 300 loop : -3.00 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 188 TYR 0.026 0.002 TYR A 300 PHE 0.026 0.002 PHE H 62 TRP 0.029 0.002 TRP A 732 HIS 0.006 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (19726) covalent geometry : angle 0.93505 / 0.43 (26941) hydrogen bonds : bond 0.04502 / 2.97 ( 583) hydrogen bonds : angle 6.11380 / 4.29 ( 1644) Misc. bond : bond 0.00995 / 0.52 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 364 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.6730 (pp20) cc_final: 0.6103 (tm-30) REVERT: A 222 HIS cc_start: 0.7068 (p90) cc_final: 0.6253 (m170) REVERT: A 434 HIS cc_start: 0.7237 (m90) cc_final: 0.6689 (m90) REVERT: A 447 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8752 (tt) REVERT: A 491 GLN cc_start: 0.6628 (tm-30) cc_final: 0.6374 (tt0) REVERT: D 59 TYR cc_start: 0.8458 (t80) cc_final: 0.7938 (t80) REVERT: D 84 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8201 (ptpp) REVERT: D 85 ASP cc_start: 0.8370 (t70) cc_final: 0.7893 (t70) REVERT: D 101 ASP cc_start: 0.7960 (t0) cc_final: 0.7587 (t0) REVERT: C 89 LYS cc_start: 0.8341 (mttt) cc_final: 0.7974 (mttt) REVERT: C 118 TYR cc_start: 0.8442 (m-80) cc_final: 0.8038 (m-10) REVERT: G 24 ASP cc_start: 0.6947 (t0) cc_final: 0.6744 (m-30) REVERT: G 103 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6803 (tp) REVERT: F 29 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8291 (mp) REVERT: F 119 GLU cc_start: 0.8240 (pp20) cc_final: 0.8013 (pp20) REVERT: F 206 ASN cc_start: 0.8006 (m-40) cc_final: 0.7798 (m110) REVERT: E 88 ASP cc_start: 0.8467 (t0) cc_final: 0.8169 (t0) REVERT: E 97 ILE cc_start: 0.9008 (mm) cc_final: 0.8782 (mt) REVERT: E 117 TYR cc_start: 0.8815 (m-80) cc_final: 0.8288 (m-80) REVERT: E 168 LYS cc_start: 0.8336 (mtmp) cc_final: 0.7992 (ptpp) REVERT: E 182 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8874 (tp) REVERT: E 190 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8224 (m-10) REVERT: E 214 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7761 (mp0) REVERT: B 11 GLN cc_start: 0.8497 (tt0) cc_final: 0.8280 (tm-30) REVERT: B 170 MET cc_start: 0.8447 (mmm) cc_final: 0.8147 (mmt) REVERT: H 305 ARG cc_start: 0.6618 (mmm160) cc_final: 0.6011 (ttm-80) outliers start: 60 outliers final: 20 residues processed: 411 average time/residue: 0.1386 time to fit residues: 85.7977 Evaluate side-chains 296 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 129 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN G 124 ASN G 137 GLN F 124 ASN B 137 HIS ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095680 restraints weight = 37892.365| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.00 r_work: 0.3142 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 19727 Z= 0.301 Angle : 0.985 15.923 26941 Z= 0.466 Chirality : 0.079 1.264 3042 Planarity : 0.005 0.059 3196 Dihedral : 12.760 174.262 3267 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.52 % Favored : 87.39 % Rotamer: Outliers : 4.45 % Allowed : 15.29 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.72 (0.16), residues: 2188 helix: -1.89 (0.16), residues: 753 sheet: -2.41 (0.29), residues: 303 loop : -2.94 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 119 TYR 0.030 0.002 TYR C 75 PHE 0.030 0.003 PHE A 246 TRP 0.028 0.003 TRP A 732 HIS 0.011 0.002 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.30 (19726) covalent geometry : angle 0.98524 / 0.47 (26941) hydrogen bonds : bond 0.04180 / 2.77 ( 583) hydrogen bonds : angle 5.77211 / 4.03 ( 1644) Misc. bond : bond 0.01016 / 0.53 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 286 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.7122 (pp20) cc_final: 0.6027 (tm-30) REVERT: A 222 HIS cc_start: 0.7120 (p90) cc_final: 0.6371 (m170) REVERT: A 326 ASP cc_start: 0.8192 (t0) cc_final: 0.7957 (t0) REVERT: A 434 HIS cc_start: 0.7239 (m90) cc_final: 0.6717 (m-70) REVERT: A 447 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8818 (tt) REVERT: A 491 GLN cc_start: 0.6871 (tm-30) cc_final: 0.6582 (tm-30) REVERT: D 15 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8357 (mtmm) REVERT: D 59 TYR cc_start: 0.8635 (t80) cc_final: 0.7868 (t80) REVERT: D 81 ILE cc_start: 0.8448 (tt) cc_final: 0.8037 (tt) REVERT: D 85 ASP cc_start: 0.8623 (t70) cc_final: 0.8128 (t0) REVERT: D 101 ASP cc_start: 0.8222 (t0) cc_final: 0.7654 (t0) REVERT: C 91 GLN cc_start: 0.8796 (mp10) cc_final: 0.8526 (mp10) REVERT: C 94 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8148 (mm-30) REVERT: F 98 PHE cc_start: 0.8447 (m-10) cc_final: 0.8136 (m-80) REVERT: F 206 ASN cc_start: 0.7967 (m-40) cc_final: 0.7520 (m110) REVERT: E 88 ASP cc_start: 0.8630 (t0) cc_final: 0.8383 (t0) REVERT: E 117 TYR cc_start: 0.8992 (m-80) cc_final: 0.8486 (m-80) REVERT: E 168 LYS cc_start: 0.8311 (mtmp) cc_final: 0.8016 (ptpp) REVERT: E 182 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8918 (tp) REVERT: B 170 MET cc_start: 0.8475 (mmm) cc_final: 0.8237 (mmt) REVERT: B 192 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: H 50 MET cc_start: 0.8431 (mmp) cc_final: 0.8204 (mmp) REVERT: H 57 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6768 (tp30) REVERT: H 92 TYR cc_start: 0.7946 (t80) cc_final: 0.7539 (t80) outliers start: 83 outliers final: 43 residues processed: 357 average time/residue: 0.1379 time to fit residues: 76.3836 Evaluate side-chains 287 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 20 optimal weight: 9.9990 chunk 109 optimal weight: 0.0570 chunk 133 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN ** D 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN B 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.120311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101073 restraints weight = 37391.641| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.04 r_work: 0.3229 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19727 Z= 0.151 Angle : 0.826 13.018 26941 Z= 0.390 Chirality : 0.067 0.990 3042 Planarity : 0.004 0.048 3196 Dihedral : 12.407 176.962 3265 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.15 % Favored : 89.76 % Rotamer: Outliers : 3.65 % Allowed : 16.79 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.19 (0.17), residues: 2188 helix: -1.22 (0.18), residues: 750 sheet: -2.27 (0.31), residues: 282 loop : -2.75 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 278 TYR 0.024 0.002 TYR D 9 PHE 0.020 0.001 PHE A 246 TRP 0.022 0.002 TRP A 732 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (19726) covalent geometry : angle 0.82639 / 0.39 (26941) hydrogen bonds : bond 0.03612 / 2.40 ( 583) hydrogen bonds : angle 5.32655 / 3.73 ( 1644) Misc. bond : bond 0.00975 / 0.51 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 283 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.6748 (pp20) cc_final: 0.5854 (tm-30) REVERT: A 222 HIS cc_start: 0.7081 (p90) cc_final: 0.6358 (m170) REVERT: A 326 ASP cc_start: 0.8123 (t0) cc_final: 0.7852 (t0) REVERT: A 434 HIS cc_start: 0.7244 (m90) cc_final: 0.6672 (m-70) REVERT: A 447 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 491 GLN cc_start: 0.6768 (tm-30) cc_final: 0.6366 (tm-30) REVERT: A 588 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8851 (tp) REVERT: D 15 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8267 (mtmm) REVERT: D 59 TYR cc_start: 0.8578 (t80) cc_final: 0.7994 (t80) REVERT: D 80 GLU cc_start: 0.7224 (tp30) cc_final: 0.6867 (tp30) REVERT: D 101 ASP cc_start: 0.8280 (t0) cc_final: 0.7712 (t0) REVERT: C 21 GLU cc_start: 0.7452 (pm20) cc_final: 0.7161 (pm20) REVERT: C 68 TYR cc_start: 0.9094 (t80) cc_final: 0.8659 (t80) REVERT: F 206 ASN cc_start: 0.7938 (m-40) cc_final: 0.7040 (m-40) REVERT: E 88 ASP cc_start: 0.8590 (t0) cc_final: 0.8342 (t70) REVERT: E 117 TYR cc_start: 0.8973 (m-80) cc_final: 0.8555 (m-80) REVERT: E 168 LYS cc_start: 0.8292 (mtmp) cc_final: 0.7970 (ptpp) REVERT: E 182 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8886 (tp) REVERT: B 170 MET cc_start: 0.8425 (mmm) cc_final: 0.8141 (mmt) REVERT: B 192 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: H 57 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6840 (tp30) REVERT: H 261 PHE cc_start: 0.7950 (t80) cc_final: 0.6979 (t80) outliers start: 68 outliers final: 38 residues processed: 339 average time/residue: 0.1355 time to fit residues: 70.5691 Evaluate side-chains 283 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 138 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN D 72 GLN F 124 ASN B 11 GLN B 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097951 restraints weight = 37591.029| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.02 r_work: 0.3176 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19727 Z= 0.213 Angle : 0.861 15.157 26941 Z= 0.406 Chirality : 0.070 1.036 3042 Planarity : 0.004 0.047 3196 Dihedral : 12.388 176.462 3263 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.93 % Favored : 87.98 % Rotamer: Outliers : 3.92 % Allowed : 16.79 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.93 (0.17), residues: 2188 helix: -0.86 (0.18), residues: 747 sheet: -2.17 (0.31), residues: 285 loop : -2.70 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 70 TYR 0.030 0.002 TYR C 75 PHE 0.023 0.002 PHE A 246 TRP 0.020 0.003 TRP A 732 HIS 0.003 0.001 HIS G 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (19726) covalent geometry : angle 0.86104 / 0.41 (26941) hydrogen bonds : bond 0.03683 / 2.45 ( 583) hydrogen bonds : angle 5.27162 / 3.68 ( 1644) Misc. bond : bond 0.00941 / 0.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 263 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 178 GLU cc_start: 0.6838 (pp20) cc_final: 0.6060 (tm-30) REVERT: A 222 HIS cc_start: 0.7147 (p90) cc_final: 0.6363 (m170) REVERT: A 326 ASP cc_start: 0.8172 (t0) cc_final: 0.7940 (t0) REVERT: A 434 HIS cc_start: 0.7248 (m90) cc_final: 0.7035 (m-70) REVERT: A 447 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8756 (tt) REVERT: A 472 LYS cc_start: 0.6146 (mmmt) cc_final: 0.5919 (mmtm) REVERT: A 491 GLN cc_start: 0.6763 (tm-30) cc_final: 0.6396 (tm-30) REVERT: A 588 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8915 (tp) REVERT: D 15 LYS cc_start: 0.8694 (mtmm) cc_final: 0.8283 (mtmm) REVERT: D 31 ASP cc_start: 0.6069 (m-30) cc_final: 0.5571 (m-30) REVERT: D 59 TYR cc_start: 0.8519 (t80) cc_final: 0.7916 (t80) REVERT: D 101 ASP cc_start: 0.8313 (t0) cc_final: 0.7672 (t0) REVERT: E 117 TYR cc_start: 0.9016 (m-80) cc_final: 0.8635 (m-80) REVERT: E 128 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7327 (mmt90) REVERT: E 168 LYS cc_start: 0.8337 (mtmp) cc_final: 0.8044 (ptpp) REVERT: E 182 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8945 (tp) REVERT: B 170 MET cc_start: 0.8358 (mmm) cc_final: 0.8115 (mmt) REVERT: B 192 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: B 229 MET cc_start: 0.8701 (mmm) cc_final: 0.8130 (mmm) REVERT: B 280 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8085 (mt) REVERT: H 57 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6798 (tp30) REVERT: H 261 PHE cc_start: 0.8006 (t80) cc_final: 0.7119 (t80) outliers start: 73 outliers final: 50 residues processed: 321 average time/residue: 0.1361 time to fit residues: 67.6333 Evaluate side-chains 298 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 628 GLN D 23 ASN D 26 ASN F 124 ASN F 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.119699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100698 restraints weight = 37115.941| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.02 r_work: 0.3224 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19727 Z= 0.158 Angle : 0.804 12.572 26941 Z= 0.379 Chirality : 0.065 0.920 3042 Planarity : 0.004 0.045 3196 Dihedral : 12.242 172.433 3263 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.92 % Favored : 89.99 % Rotamer: Outliers : 3.59 % Allowed : 17.44 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.67 (0.17), residues: 2188 helix: -0.51 (0.19), residues: 748 sheet: -2.14 (0.31), residues: 286 loop : -2.61 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 512 TYR 0.043 0.002 TYR B 157 PHE 0.020 0.001 PHE A 246 TRP 0.019 0.002 TRP A 732 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (19726) covalent geometry : angle 0.80448 / 0.38 (26941) hydrogen bonds : bond 0.03512 / 2.36 ( 583) hydrogen bonds : angle 5.08509 / 3.56 ( 1644) Misc. bond : bond 0.00984 / 0.52 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 264 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7463 (tptt) cc_final: 0.6490 (ttmm) REVERT: A 178 GLU cc_start: 0.6612 (pp20) cc_final: 0.5950 (tm-30) REVERT: A 222 HIS cc_start: 0.7123 (p90) cc_final: 0.6377 (m-70) REVERT: A 326 ASP cc_start: 0.8163 (t0) cc_final: 0.7892 (t0) REVERT: A 434 HIS cc_start: 0.7228 (m90) cc_final: 0.6911 (m-70) REVERT: A 447 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8732 (tt) REVERT: A 472 LYS cc_start: 0.6302 (mmmt) cc_final: 0.5978 (mmtm) REVERT: A 491 GLN cc_start: 0.6788 (tm-30) cc_final: 0.6432 (tm-30) REVERT: D 15 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8262 (mtmm) REVERT: D 31 ASP cc_start: 0.6109 (m-30) cc_final: 0.5614 (m-30) REVERT: D 59 TYR cc_start: 0.8462 (t80) cc_final: 0.7859 (t80) REVERT: D 80 GLU cc_start: 0.7340 (tp30) cc_final: 0.6974 (tp30) REVERT: D 101 ASP cc_start: 0.8347 (t0) cc_final: 0.7682 (t0) REVERT: C 94 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7934 (mt-10) REVERT: E 88 ASP cc_start: 0.8535 (t0) cc_final: 0.8292 (t70) REVERT: E 117 TYR cc_start: 0.8990 (m-80) cc_final: 0.8537 (m-80) REVERT: E 168 LYS cc_start: 0.8404 (mtmp) cc_final: 0.8030 (ptpp) REVERT: E 182 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8908 (tp) REVERT: B 170 MET cc_start: 0.8378 (mmm) cc_final: 0.8102 (mmt) REVERT: B 192 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: B 229 MET cc_start: 0.8644 (mmm) cc_final: 0.8013 (mmm) REVERT: B 280 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8045 (mt) REVERT: H 57 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6803 (tp30) REVERT: H 261 PHE cc_start: 0.8046 (t80) cc_final: 0.7752 (t80) outliers start: 67 outliers final: 49 residues processed: 319 average time/residue: 0.1336 time to fit residues: 66.3921 Evaluate side-chains 296 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 138 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 1 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN G 65 ASN F 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095639 restraints weight = 37459.954| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.97 r_work: 0.3141 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 19727 Z= 0.276 Angle : 0.903 14.591 26941 Z= 0.427 Chirality : 0.073 1.114 3042 Planarity : 0.004 0.049 3196 Dihedral : 12.408 173.870 3263 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.75 % Favored : 87.16 % Rotamer: Outliers : 4.35 % Allowed : 17.27 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.72 (0.17), residues: 2188 helix: -0.53 (0.19), residues: 746 sheet: -2.26 (0.29), residues: 320 loop : -2.62 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 140 TYR 0.063 0.002 TYR A 573 PHE 0.027 0.002 PHE A 246 TRP 0.017 0.002 TRP A 732 HIS 0.005 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.28 (19726) covalent geometry : angle 0.90303 / 0.43 (26941) hydrogen bonds : bond 0.03887 / 2.57 ( 583) hydrogen bonds : angle 5.29164 / 3.68 ( 1644) Misc. bond : bond 0.01015 / 0.53 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 253 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 HIS cc_start: 0.7176 (p90) cc_final: 0.6346 (m90) REVERT: A 326 ASP cc_start: 0.8290 (t0) cc_final: 0.8085 (t0) REVERT: A 447 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8783 (tt) REVERT: A 491 GLN cc_start: 0.6776 (tm-30) cc_final: 0.6467 (tm-30) REVERT: A 538 GLN cc_start: 0.6838 (pm20) cc_final: 0.6630 (pm20) REVERT: D 15 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8263 (mtmm) REVERT: D 59 TYR cc_start: 0.8474 (t80) cc_final: 0.7775 (t80) REVERT: D 101 ASP cc_start: 0.8350 (t0) cc_final: 0.7659 (t0) REVERT: E 88 ASP cc_start: 0.8672 (t0) cc_final: 0.8440 (t70) REVERT: E 117 TYR cc_start: 0.8989 (m-80) cc_final: 0.8641 (m-80) REVERT: E 128 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7445 (mmt90) REVERT: E 168 LYS cc_start: 0.8405 (mtmp) cc_final: 0.8138 (ptpp) REVERT: E 182 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9000 (tp) REVERT: B 170 MET cc_start: 0.8405 (mmm) cc_final: 0.8193 (mmt) REVERT: B 192 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: B 229 MET cc_start: 0.8565 (mmm) cc_final: 0.7955 (mmm) REVERT: B 280 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8215 (mt) REVERT: H 57 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6851 (tp30) REVERT: H 261 PHE cc_start: 0.8112 (t80) cc_final: 0.7902 (t80) outliers start: 81 outliers final: 57 residues processed: 320 average time/residue: 0.1393 time to fit residues: 69.6378 Evaluate side-chains 290 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 228 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 128 ARG Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 0.0770 chunk 168 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 192 optimal weight: 0.0030 chunk 92 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 1.1552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN G 65 ASN F 124 ASN E 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.122014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.103391 restraints weight = 37272.448| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.02 r_work: 0.3265 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19727 Z= 0.135 Angle : 0.801 12.405 26941 Z= 0.379 Chirality : 0.062 0.905 3042 Planarity : 0.004 0.044 3196 Dihedral : 12.019 168.478 3263 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.37 % Favored : 90.54 % Rotamer: Outliers : 3.38 % Allowed : 19.10 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.39 (0.18), residues: 2188 helix: -0.18 (0.19), residues: 753 sheet: -2.14 (0.29), residues: 323 loop : -2.48 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 65 TYR 0.060 0.002 TYR B 157 PHE 0.018 0.001 PHE A 246 TRP 0.018 0.002 TRP A 732 HIS 0.006 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (19726) covalent geometry : angle 0.80131 / 0.38 (26941) hydrogen bonds : bond 0.03509 / 2.35 ( 583) hydrogen bonds : angle 4.97463 / 3.48 ( 1644) Misc. bond : bond 0.00972 / 0.51 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.7860 (m-80) cc_final: 0.7034 (t80) REVERT: A 129 ASN cc_start: 0.7905 (p0) cc_final: 0.7529 (p0) REVERT: A 222 HIS cc_start: 0.7007 (p90) cc_final: 0.6320 (m-70) REVERT: A 326 ASP cc_start: 0.8186 (t0) cc_final: 0.7869 (t0) REVERT: A 434 HIS cc_start: 0.7307 (m90) cc_final: 0.6582 (m170) REVERT: A 447 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 491 GLN cc_start: 0.6815 (tm-30) cc_final: 0.6501 (tm-30) REVERT: A 508 LEU cc_start: 0.8641 (pp) cc_final: 0.8128 (mt) REVERT: D 15 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8238 (mtmm) REVERT: D 59 TYR cc_start: 0.8250 (t80) cc_final: 0.7806 (t80) REVERT: D 80 GLU cc_start: 0.7397 (tp30) cc_final: 0.6874 (tp30) REVERT: D 88 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7233 (tm-30) REVERT: D 101 ASP cc_start: 0.8315 (t0) cc_final: 0.7641 (t0) REVERT: G 137 GLN cc_start: 0.8686 (mt0) cc_final: 0.8440 (mt0) REVERT: E 88 ASP cc_start: 0.8380 (t0) cc_final: 0.8147 (t70) REVERT: E 117 TYR cc_start: 0.8969 (m-80) cc_final: 0.8593 (m-80) REVERT: E 168 LYS cc_start: 0.8442 (mtmp) cc_final: 0.8097 (ptpp) REVERT: E 182 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8976 (tp) REVERT: B 170 MET cc_start: 0.8342 (mmm) cc_final: 0.8116 (mmt) REVERT: B 192 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7434 (m-30) REVERT: B 229 MET cc_start: 0.8610 (mmm) cc_final: 0.7942 (mmm) REVERT: B 280 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7994 (mt) REVERT: H 57 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6709 (tp30) REVERT: H 113 GLU cc_start: 0.8296 (pt0) cc_final: 0.7674 (mp0) REVERT: H 261 PHE cc_start: 0.8076 (t80) cc_final: 0.7755 (t80) outliers start: 63 outliers final: 42 residues processed: 329 average time/residue: 0.1451 time to fit residues: 74.4336 Evaluate side-chains 288 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 138 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 160 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN C 106 GLN G 65 ASN G 162 GLN F 124 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097253 restraints weight = 37270.098| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.99 r_work: 0.3167 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19727 Z= 0.240 Angle : 0.879 12.924 26941 Z= 0.415 Chirality : 0.069 1.046 3042 Planarity : 0.004 0.061 3196 Dihedral : 12.224 170.233 3263 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.39 % Favored : 87.52 % Rotamer: Outliers : 3.11 % Allowed : 19.37 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.53 (0.18), residues: 2188 helix: -0.38 (0.19), residues: 769 sheet: -2.24 (0.29), residues: 322 loop : -2.50 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 81 TYR 0.059 0.002 TYR A 573 PHE 0.024 0.002 PHE A 246 TRP 0.014 0.002 TRP A 732 HIS 0.006 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (19726) covalent geometry : angle 0.87893 / 0.41 (26941) hydrogen bonds : bond 0.03735 / 2.48 ( 583) hydrogen bonds : angle 5.17165 / 3.60 ( 1644) Misc. bond : bond 0.00980 / 0.52 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7935 (p0) cc_final: 0.7509 (p0) REVERT: A 222 HIS cc_start: 0.7067 (p90) cc_final: 0.6311 (m-70) REVERT: A 326 ASP cc_start: 0.8317 (t0) cc_final: 0.8059 (t0) REVERT: A 363 TYR cc_start: 0.6049 (t80) cc_final: 0.5773 (t80) REVERT: A 434 HIS cc_start: 0.7366 (m90) cc_final: 0.6627 (m170) REVERT: A 447 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8767 (tt) REVERT: A 491 GLN cc_start: 0.6723 (tm-30) cc_final: 0.6435 (tm-30) REVERT: D 59 TYR cc_start: 0.8414 (t80) cc_final: 0.7851 (t80) REVERT: D 80 GLU cc_start: 0.7338 (tp30) cc_final: 0.6863 (tp30) REVERT: D 101 ASP cc_start: 0.8348 (t0) cc_final: 0.7724 (t0) REVERT: E 88 ASP cc_start: 0.8563 (t0) cc_final: 0.8312 (t0) REVERT: E 117 TYR cc_start: 0.9001 (m-80) cc_final: 0.8615 (m-80) REVERT: E 168 LYS cc_start: 0.8426 (mtmp) cc_final: 0.8112 (ptpp) REVERT: E 182 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9002 (tp) REVERT: B 170 MET cc_start: 0.8467 (mmm) cc_final: 0.8232 (mmt) REVERT: B 192 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: B 229 MET cc_start: 0.8602 (mmm) cc_final: 0.7946 (mmm) REVERT: B 280 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8164 (mt) REVERT: H 57 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6852 (tp30) REVERT: H 261 PHE cc_start: 0.8168 (t80) cc_final: 0.7933 (t80) outliers start: 58 outliers final: 44 residues processed: 296 average time/residue: 0.1394 time to fit residues: 65.0364 Evaluate side-chains 290 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 202 optimal weight: 8.9990 chunk 127 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 chunk 154 optimal weight: 0.2980 chunk 142 optimal weight: 7.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN G 65 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.124464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106292 restraints weight = 37171.530| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.96 r_work: 0.3318 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19727 Z= 0.128 Angle : 0.787 12.606 26941 Z= 0.372 Chirality : 0.060 0.892 3042 Planarity : 0.004 0.049 3196 Dihedral : 11.825 165.907 3263 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.10 % Favored : 90.86 % Rotamer: Outliers : 2.09 % Allowed : 20.60 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.27 (0.18), residues: 2188 helix: -0.02 (0.20), residues: 750 sheet: -2.11 (0.28), residues: 331 loop : -2.43 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 65 TYR 0.051 0.002 TYR B 157 PHE 0.015 0.001 PHE A 246 TRP 0.016 0.002 TRP A 38 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (19726) covalent geometry : angle 0.78735 / 0.37 (26941) hydrogen bonds : bond 0.03472 / 2.32 ( 583) hydrogen bonds : angle 4.88996 / 3.42 ( 1644) Misc. bond : bond 0.00908 / 0.48 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 PHE cc_start: 0.7984 (m-80) cc_final: 0.7441 (t80) REVERT: A 128 LEU cc_start: 0.7834 (tt) cc_final: 0.7378 (tp) REVERT: A 129 ASN cc_start: 0.7843 (p0) cc_final: 0.7495 (p0) REVERT: A 222 HIS cc_start: 0.6914 (p90) cc_final: 0.6235 (m-70) REVERT: A 326 ASP cc_start: 0.8084 (t0) cc_final: 0.7759 (t0) REVERT: A 434 HIS cc_start: 0.7223 (m90) cc_final: 0.6482 (m170) REVERT: A 447 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8621 (tt) REVERT: A 491 GLN cc_start: 0.6752 (tm-30) cc_final: 0.6448 (tm-30) REVERT: A 508 LEU cc_start: 0.8609 (pp) cc_final: 0.8073 (mt) REVERT: D 15 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8343 (mtmt) REVERT: D 59 TYR cc_start: 0.8208 (t80) cc_final: 0.7830 (t80) REVERT: D 62 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8450 (tt) REVERT: D 99 ILE cc_start: 0.8397 (tt) cc_final: 0.7503 (tt) REVERT: D 101 ASP cc_start: 0.8249 (t0) cc_final: 0.7651 (t0) REVERT: C 68 TYR cc_start: 0.8906 (t80) cc_final: 0.8621 (t80) REVERT: E 88 ASP cc_start: 0.8316 (t0) cc_final: 0.7999 (t70) REVERT: E 91 PHE cc_start: 0.7965 (m-10) cc_final: 0.7685 (m-10) REVERT: E 117 TYR cc_start: 0.8926 (m-80) cc_final: 0.8542 (m-80) REVERT: E 168 LYS cc_start: 0.8371 (mtmp) cc_final: 0.8012 (ptpp) REVERT: B 170 MET cc_start: 0.8349 (mmm) cc_final: 0.8105 (mmt) REVERT: B 192 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: B 229 MET cc_start: 0.8595 (mmm) cc_final: 0.7836 (mmm) REVERT: B 280 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7989 (mt) REVERT: H 57 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6708 (tp30) REVERT: H 261 PHE cc_start: 0.7937 (t80) cc_final: 0.7668 (t80) outliers start: 39 outliers final: 30 residues processed: 294 average time/residue: 0.1402 time to fit residues: 64.8578 Evaluate side-chains 274 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain H residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 103 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN C 72 GLN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN B 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102309 restraints weight = 37102.219| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.99 r_work: 0.3249 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19727 Z= 0.172 Angle : 0.810 12.977 26941 Z= 0.383 Chirality : 0.063 0.860 3042 Planarity : 0.004 0.045 3196 Dihedral : 11.846 167.526 3263 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.47 % Favored : 89.49 % Rotamer: Outliers : 2.15 % Allowed : 21.30 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.24 (0.18), residues: 2188 helix: -0.07 (0.20), residues: 762 sheet: -2.13 (0.29), residues: 322 loop : -2.36 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 81 TYR 0.048 0.002 TYR B 157 PHE 0.024 0.002 PHE A 183 TRP 0.013 0.002 TRP A 732 HIS 0.006 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (19726) covalent geometry : angle 0.81018 / 0.38 (26941) hydrogen bonds : bond 0.03502 / 2.33 ( 583) hydrogen bonds : angle 4.96606 / 3.46 ( 1644) Misc. bond : bond 0.00902 / 0.47 ( 1) =============================================================================== Job complete usr+sys time: 4517.37 seconds wall clock time: 78 minutes 29.66 seconds (4709.66 seconds total)