Starting phenix.real_space_refine on Sat Sep 12 22:58:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ig0_9660/09_2026/6ig0_9660.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ig0_9660/09_2026/6ig0_9660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2026/6ig0_9660.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2026/6ig0_9660.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2026/6ig0_9660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2026/6ig0_9660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2026/6ig0_9660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2026/6ig0_9660.map" } resolution = 3.37 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 72 5.49 5 Mg 2 5.21 5 S 37 5.16 5 C 12090 2.51 5 N 3296 2.21 5 O 3856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 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: 19354 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5812 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 8, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1697 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1626 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2334 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2748 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 17, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "N" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 715 Classifications: {'RNAv2': 33} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 20, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 2, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2929 SG CYS A 401 57.965 30.672 66.675 1.00 74.37 S ATOM 2952 SG CYS A 404 55.630 31.804 64.016 1.00 70.96 S ATOM 3074 SG CYS A 419 58.898 30.714 62.945 1.00 75.02 S ATOM 3096 SG CYS A 422 58.767 34.241 63.931 1.00 70.14 S Time building chain proxies: 4.39, per 1000 atoms: 0.23 Number of scatterers: 19354 At special positions: 0 Unit cell: (92.56, 136.24, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 37 16.00 P 72 15.00 Mg 2 11.99 O 3856 8.00 N 3296 7.00 C 12090 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 794.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 401 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 422 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 404 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 419 " Number of angles added : 6 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4262 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 23 sheets defined 38.2% alpha, 10.4% beta 20 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.610A pdb=" N TYR A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.595A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.754A pdb=" N VAL A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.981A pdb=" N GLN A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.521A pdb=" N THR A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.250A pdb=" N TYR A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.855A pdb=" N ASN A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 197 through 220 removed outlier: 3.540A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 265 through 291 removed outlier: 3.726A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 336 removed outlier: 3.947A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 368 through 378 Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.663A pdb=" N LEU A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.614A pdb=" N GLY A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 541 through 558 removed outlier: 3.664A pdb=" N SER A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 585 through 603 removed outlier: 3.791A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 637 removed outlier: 3.633A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.589A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 removed outlier: 3.913A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 730 removed outlier: 3.737A pdb=" N PHE A 722 " --> pdb=" O ASP A 718 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 753 Processing helix chain 'D' and resid 8 through 20 Processing helix chain 'D' and resid 36 through 52 removed outlier: 3.734A pdb=" N LEU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 removed outlier: 3.851A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 80 removed outlier: 3.575A pdb=" N ALA D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.630A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 97 removed outlier: 3.885A pdb=" N LYS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 36 through 52 removed outlier: 3.733A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.851A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 80 removed outlier: 3.575A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.629A pdb=" N GLU C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.886A pdb=" N LYS C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'G' and resid 49 through 59 removed outlier: 3.803A pdb=" N LYS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 112 Processing helix chain 'G' and resid 161 through 178 removed outlier: 4.010A pdb=" N GLU G 165 " --> pdb=" O ASN G 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS G 175 " --> pdb=" O ARG G 171 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 176 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU G 178 " --> pdb=" O LEU G 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.620A pdb=" N LEU F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 removed outlier: 4.023A pdb=" N ASP F 75 " --> pdb=" O PRO F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.702A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 removed outlier: 3.644A pdb=" N ASP F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 178 removed outlier: 3.793A pdb=" N PHE F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU F 178 " --> pdb=" O LEU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.505A pdb=" N ARG F 188 " --> pdb=" O SER F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 217 removed outlier: 3.883A pdb=" N LEU F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 54 through 64 removed outlier: 3.670A pdb=" N LEU E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.973A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 176 Processing helix chain 'E' and resid 209 through 217 removed outlier: 3.553A pdb=" N ASN E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU E 215 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.889A pdb=" N ILE B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.637A pdb=" N PHE B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 3.646A pdb=" N ARG B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.702A pdb=" N MET B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 52 Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.686A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 75 through 82 removed outlier: 3.592A pdb=" N LEU H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.719A pdb=" N ALA H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR H 143 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 179 through 182 Processing helix chain 'H' and resid 236 through 245 removed outlier: 3.800A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU H 244 " --> pdb=" O GLY H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 259 removed outlier: 4.402A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 259 " --> pdb=" O LYS H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 270 removed outlier: 3.827A pdb=" N LYS H 269 " --> pdb=" O PRO H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.683A pdb=" N ARG H 302 " --> pdb=" O LEU H 299 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR H 303 " --> pdb=" O GLN H 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 246 removed outlier: 3.652A pdb=" N ALA A 306 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.635A pdb=" N TYR A 340 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 448 removed outlier: 6.635A pdb=" N ALA A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 490 through 491 removed outlier: 4.047A pdb=" N TYR A 490 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 569 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER A 584 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE A 571 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 582 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 612 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER A 643 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 152 through 155 removed outlier: 6.572A pdb=" N LYS G 5 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 102 through 103 removed outlier: 4.052A pdb=" N PHE G 102 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 118 through 122 Processing sheet with id=AA9, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.679A pdb=" N LEU F 151 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE F 8 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS F 5 " --> pdb=" O VAL F 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 146 through 149 Processing sheet with id=AB2, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB3, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.740A pdb=" N LEU E 151 " --> pdb=" O PHE E 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.740A pdb=" N LEU E 151 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS E 5 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 203 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN E 11 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN E 197 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG E 13 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE E 195 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 123 removed outlier: 3.585A pdb=" N GLU E 123 " --> pdb=" O ARG E 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.612A pdb=" N VAL B 158 " --> pdb=" O TYR B 6 " (cutoff:3.500A) 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 127 through 131 removed outlier: 3.840A pdb=" N VAL B 127 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 149 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 267 Processing sheet with id=AC1, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AC2, first strand: chain 'H' and resid 227 through 230 Processing sheet with id=AC3, first strand: chain 'H' and resid 37 through 41 Processing sheet with id=AC4, first strand: chain 'H' and resid 184 through 186 Processing sheet with id=AC5, first strand: chain 'H' and resid 211 through 214 removed outlier: 4.204A pdb=" N LYS H 211 " --> pdb=" O SER H 206 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3727 1.32 - 1.45: 5207 1.45 - 1.57: 10720 1.57 - 1.69: 140 1.69 - 1.81: 66 Bond restraints: 19860 Sorted by residual: bond pdb=" C4 ATP A 802 " pdb=" C5 ATP A 802 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.50e+01 bond pdb=" C4 ATP A 803 " pdb=" C5 ATP A 803 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C5 ATP A 802 " pdb=" C6 ATP A 802 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C5 ATP A 803 " pdb=" C6 ATP A 803 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C8 ATP A 803 " pdb=" N7 ATP A 803 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.18e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 26749 4.16 - 8.33: 340 8.33 - 12.49: 35 12.49 - 16.65: 7 16.65 - 20.82: 2 Bond angle restraints: 27133 Sorted by residual: angle pdb=" PB ATP A 802 " pdb=" O3B ATP A 802 " pdb=" PG ATP A 802 " ideal model delta sigma weight residual 139.87 123.73 16.14 1.00e+00 1.00e+00 2.60e+02 angle pdb=" PA ATP A 802 " pdb=" O3A ATP A 802 " pdb=" PB ATP A 802 " ideal model delta sigma weight residual 136.83 121.65 15.18 1.00e+00 1.00e+00 2.31e+02 angle pdb=" PB ATP A 803 " pdb=" O3B ATP A 803 " pdb=" PG ATP A 803 " ideal model delta sigma weight residual 139.87 126.01 13.86 1.00e+00 1.00e+00 1.92e+02 angle pdb=" PA ATP A 803 " pdb=" O3A ATP A 803 " pdb=" PB ATP A 803 " ideal model delta sigma weight residual 136.83 123.96 12.87 1.00e+00 1.00e+00 1.66e+02 angle pdb=" N ARG H 219 " pdb=" CA ARG H 219 " pdb=" C ARG H 219 " ideal model delta sigma weight residual 111.39 126.13 -14.74 1.38e+00 5.25e-01 1.14e+02 ... (remaining 27128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.13: 11336 29.13 - 58.26: 358 58.26 - 87.39: 54 87.39 - 116.53: 0 116.53 - 145.66: 1 Dihedral angle restraints: 11749 sinusoidal: 5141 harmonic: 6608 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 -40.52 76.87 1 3.10e+00 1.04e-01 7.72e+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 -40.23 76.57 1 3.10e+00 1.04e-01 7.67e+02 dihedral pdb=" C4' G N 9 " pdb=" C3' G N 9 " pdb=" C2' G N 9 " pdb=" C1' G N 9 " ideal model delta sinusoidal sigma weight residual 36.34 -38.83 75.17 1 3.10e+00 1.04e-01 7.43e+02 ... (remaining 11746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2817 0.132 - 0.264: 202 0.264 - 0.396: 39 0.396 - 0.528: 3 0.528 - 0.659: 1 Chirality restraints: 3062 Sorted by residual: chirality pdb=" CA TYR H 218 " pdb=" N TYR H 218 " pdb=" C TYR H 218 " pdb=" CB TYR H 218 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA PRO H 160 " pdb=" N PRO H 160 " pdb=" C PRO H 160 " pdb=" CB PRO H 160 " both_signs ideal model delta sigma weight residual False 2.72 2.21 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA TYR B 78 " pdb=" N TYR B 78 " pdb=" C TYR B 78 " pdb=" CB TYR B 78 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 3059 not shown) Planarity restraints: 3243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 154 " -0.020 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C ASN H 154 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN H 154 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP H 155 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 163 " 0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ASN H 163 " -0.068 2.00e-02 2.50e+03 pdb=" O ASN H 163 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS H 164 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.031 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 732 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.010 2.00e-02 2.50e+03 ... (remaining 3240 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 6 1.86 - 2.62: 333 2.62 - 3.38: 25599 3.38 - 4.14: 48867 4.14 - 4.90: 88496 Nonbonded interactions: 163301 Sorted by model distance: nonbonded pdb=" NH1 ARG E 81 " pdb=" OE1 GLN E 162 " model vdw 1.102 3.120 nonbonded pdb=" CZ ARG E 81 " pdb=" OE1 GLN E 162 " model vdw 1.434 3.270 nonbonded pdb=" NH1 ARG E 81 " pdb=" CD GLN E 162 " model vdw 1.711 3.350 nonbonded pdb=" CD2 LEU A 749 " pdb=" CD1 ILE E 29 " model vdw 1.748 3.880 nonbonded pdb=" O SER B 264 " pdb=" CE1 PHE B 266 " model vdw 1.804 3.340 ... (remaining 163296 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 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 217)) selection = (chain 'F' and (resid 2 through 66 or resid 76 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 or (r \ esid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 t \ hrough 217)) selection = (chain 'G' and (resid 2 through 66 or resid 76 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.500 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.164 19867 Z= 0.441 Angle : 1.250 33.042 27139 Z= 0.691 Chirality : 0.081 0.659 3062 Planarity : 0.006 0.070 3243 Dihedral : 14.038 145.658 7487 Min Nonbonded Distance : 1.102 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.44 % Favored : 89.43 % Rotamer: Outliers : 1.40 % Allowed : 7.16 % Favored : 91.44 % Cbeta Deviations : 0.23 % 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: -5.65 (0.12), residues: 2232 helix: -4.34 (0.08), residues: 787 sheet: -3.24 (0.23), residues: 372 loop : -3.40 (0.14), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 57 TYR 0.031 0.003 TYR A 149 PHE 0.043 0.004 PHE F 98 TRP 0.064 0.006 TRP A 732 HIS 0.011 0.002 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.44 (19860) covalent geometry : angle 1.22630 / 0.69 (27133) hydrogen bonds : bond 0.28698 / 18.99 ( 624) hydrogen bonds : angle 10.42501 / 7.25 ( 1732) metal coordination : bond 0.11395 / 5.68 ( 4) metal coordination : angle 16.41979 / 8.85 ( 6) Misc. bond : bond 0.00376 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 616 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 TYR cc_start: 0.7350 (m-80) cc_final: 0.6901 (m-80) REVERT: A 205 THR cc_start: 0.8582 (m) cc_final: 0.8335 (p) REVERT: A 384 TYR cc_start: 0.7803 (t80) cc_final: 0.7102 (t80) REVERT: A 415 ASP cc_start: 0.6442 (p0) cc_final: 0.5814 (t0) REVERT: A 490 TYR cc_start: 0.7375 (t80) cc_final: 0.7060 (t80) REVERT: A 521 ASP cc_start: 0.8128 (m-30) cc_final: 0.7774 (m-30) REVERT: D 14 GLU cc_start: 0.7780 (tt0) cc_final: 0.7450 (tt0) REVERT: D 34 PHE cc_start: 0.8298 (m-10) cc_final: 0.8043 (m-80) REVERT: D 63 LEU cc_start: 0.7572 (pt) cc_final: 0.6974 (tt) REVERT: D 85 ASP cc_start: 0.6754 (t70) cc_final: 0.5413 (t0) REVERT: D 89 LYS cc_start: 0.8022 (mptm) cc_final: 0.7762 (mptp) REVERT: D 91 GLN cc_start: 0.7418 (pm20) cc_final: 0.6850 (pm20) REVERT: G 137 GLN cc_start: 0.7877 (mt0) cc_final: 0.7636 (mt0) REVERT: F 62 LYS cc_start: 0.8628 (mttt) cc_final: 0.8422 (mmtt) REVERT: F 74 ASP cc_start: 0.8182 (t70) cc_final: 0.7936 (t70) REVERT: F 137 GLN cc_start: 0.8182 (mt0) cc_final: 0.7684 (mt0) REVERT: E 9 SER cc_start: 0.8450 (m) cc_final: 0.8247 (t) REVERT: E 39 ASP cc_start: 0.8310 (t0) cc_final: 0.8092 (t0) REVERT: E 88 ASP cc_start: 0.7542 (t0) cc_final: 0.7265 (t0) REVERT: E 144 ASN cc_start: 0.7770 (p0) cc_final: 0.7534 (m110) REVERT: E 167 PHE cc_start: 0.7379 (m-10) cc_final: 0.6654 (m-80) REVERT: B 229 MET cc_start: 0.8543 (mmt) cc_final: 0.8298 (mmm) REVERT: B 276 ASP cc_start: 0.7980 (t0) cc_final: 0.6506 (t0) REVERT: B 278 ARG cc_start: 0.8014 (ptp-170) cc_final: 0.7122 (ptp-170) REVERT: H 22 ASN cc_start: 0.8292 (t0) cc_final: 0.7877 (t0) REVERT: H 86 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5031 (mp0) REVERT: H 89 PHE cc_start: 0.6518 (m-80) cc_final: 0.5499 (m-80) outliers start: 26 outliers final: 11 residues processed: 637 average time/residue: 0.1856 time to fit residues: 168.4444 Evaluate side-chains 324 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 312 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 166 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 135 ASN A 257 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS A 639 ASN A 661 ASN A 735 ASN G 134 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN F 33 ASN F 144 ASN F 213 ASN E 11 GLN E 134 ASN B 81 HIS ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 288 ASN H 154 ASN H 338 ASN H 339 HIS H 349 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.131703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111027 restraints weight = 35795.078| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.23 r_work: 0.3353 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19867 Z= 0.173 Angle : 0.970 17.519 27139 Z= 0.453 Chirality : 0.079 1.464 3062 Planarity : 0.005 0.084 3243 Dihedral : 12.650 154.750 3295 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.65 % Favored : 91.31 % Rotamer: Outliers : 3.77 % Allowed : 12.86 % Favored : 83.37 % 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: -4.48 (0.14), residues: 2232 helix: -2.80 (0.13), residues: 823 sheet: -2.85 (0.26), residues: 318 loop : -3.14 (0.15), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 119 TYR 0.029 0.002 TYR C 59 PHE 0.028 0.002 PHE A 591 TRP 0.032 0.002 TRP A 732 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (19860) covalent geometry : angle 0.96885 / 0.45 (27133) hydrogen bonds : bond 0.04958 / 3.38 ( 624) hydrogen bonds : angle 5.68964 / 3.99 ( 1732) metal coordination : bond 0.00493 / 0.25 ( 4) metal coordination : angle 3.46729 / 1.80 ( 6) Misc. bond : bond 0.00266 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 396 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.7146 (m-80) cc_final: 0.6774 (m-80) REVERT: A 198 LEU cc_start: 0.8646 (tp) cc_final: 0.8370 (tp) REVERT: A 202 SER cc_start: 0.8545 (m) cc_final: 0.8288 (p) REVERT: A 205 THR cc_start: 0.8842 (m) cc_final: 0.8537 (p) REVERT: A 235 PHE cc_start: 0.7451 (t80) cc_final: 0.7212 (t80) REVERT: A 285 ASP cc_start: 0.6956 (m-30) cc_final: 0.6707 (m-30) REVERT: A 289 ASP cc_start: 0.7953 (p0) cc_final: 0.7596 (m-30) REVERT: A 300 TYR cc_start: 0.7572 (t80) cc_final: 0.7056 (t80) REVERT: A 373 MET cc_start: 0.8537 (ttt) cc_final: 0.8162 (ttt) REVERT: A 384 TYR cc_start: 0.7836 (t80) cc_final: 0.7527 (t80) REVERT: A 415 ASP cc_start: 0.6672 (p0) cc_final: 0.5696 (t0) REVERT: A 490 TYR cc_start: 0.7312 (t80) cc_final: 0.7110 (t80) REVERT: A 552 MET cc_start: 0.8968 (mmp) cc_final: 0.8704 (mmp) REVERT: A 578 ASP cc_start: 0.7480 (t70) cc_final: 0.7192 (m-30) REVERT: A 686 TYR cc_start: 0.8004 (t80) cc_final: 0.7692 (t80) REVERT: D 21 GLU cc_start: 0.8218 (pm20) cc_final: 0.8014 (pm20) REVERT: D 34 PHE cc_start: 0.8578 (m-10) cc_final: 0.8287 (m-80) REVERT: D 55 LYS cc_start: 0.8610 (mptt) cc_final: 0.8188 (mptt) REVERT: D 58 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7720 (mp0) REVERT: D 63 LEU cc_start: 0.7471 (pt) cc_final: 0.6742 (tt) REVERT: D 70 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8085 (ttp80) REVERT: D 85 ASP cc_start: 0.7352 (t70) cc_final: 0.7063 (t0) REVERT: C 21 GLU cc_start: 0.7425 (pm20) cc_final: 0.7146 (tp30) REVERT: C 87 ILE cc_start: 0.8628 (pt) cc_final: 0.8375 (pt) REVERT: C 102 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.7034 (ttm-80) REVERT: C 110 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8025 (mtt90) REVERT: G 67 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8198 (mtpp) REVERT: G 176 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8514 (tt) REVERT: F 74 ASP cc_start: 0.8580 (t70) cc_final: 0.8152 (t70) REVERT: E 9 SER cc_start: 0.8498 (m) cc_final: 0.8163 (t) REVERT: E 39 ASP cc_start: 0.8641 (t0) cc_final: 0.8412 (t0) REVERT: E 160 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: E 167 PHE cc_start: 0.7550 (m-10) cc_final: 0.6895 (m-80) REVERT: B 229 MET cc_start: 0.8483 (mmt) cc_final: 0.8205 (mmm) REVERT: B 231 ASP cc_start: 0.7189 (t0) cc_final: 0.6964 (t0) REVERT: B 238 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7802 (tptm) REVERT: H 12 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8744 (tm) REVERT: H 22 ASN cc_start: 0.8606 (t0) cc_final: 0.8192 (t0) REVERT: H 83 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7582 (mmm160) outliers start: 70 outliers final: 29 residues processed: 445 average time/residue: 0.1646 time to fit residues: 109.1836 Evaluate side-chains 336 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 34 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN A 661 ASN D 42 ASN G 85 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN H 151 ASN ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108085 restraints weight = 36129.517| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.10 r_work: 0.3292 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19867 Z= 0.208 Angle : 0.877 15.324 27139 Z= 0.414 Chirality : 0.071 1.545 3062 Planarity : 0.004 0.046 3243 Dihedral : 12.736 165.842 3283 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.59 % Rotamer: Outliers : 4.25 % Allowed : 15.82 % Favored : 79.92 % 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: -3.72 (0.15), residues: 2232 helix: -1.82 (0.15), residues: 825 sheet: -2.62 (0.27), residues: 318 loop : -2.94 (0.16), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 119 TYR 0.020 0.002 TYR C 68 PHE 0.033 0.002 PHE A 348 TRP 0.023 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (19860) covalent geometry : angle 0.87524 / 0.41 (27133) hydrogen bonds : bond 0.04368 / 2.96 ( 624) hydrogen bonds : angle 5.11299 / 3.59 ( 1732) metal coordination : bond 0.00473 / 0.24 ( 4) metal coordination : angle 3.37653 / 1.63 ( 6) Misc. bond : bond 0.00094 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 326 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.7288 (m-80) cc_final: 0.6907 (m-80) REVERT: A 130 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6822 (mm) REVERT: A 198 LEU cc_start: 0.8666 (tp) cc_final: 0.8415 (tp) REVERT: A 202 SER cc_start: 0.8595 (m) cc_final: 0.8357 (p) REVERT: A 205 THR cc_start: 0.8928 (m) cc_final: 0.8599 (p) REVERT: A 235 PHE cc_start: 0.7568 (t80) cc_final: 0.7275 (t80) REVERT: A 300 TYR cc_start: 0.7575 (t80) cc_final: 0.7216 (t80) REVERT: A 373 MET cc_start: 0.8600 (ttt) cc_final: 0.8079 (ttt) REVERT: A 384 TYR cc_start: 0.8096 (t80) cc_final: 0.7699 (t80) REVERT: A 395 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8038 (mtpt) REVERT: A 415 ASP cc_start: 0.6648 (p0) cc_final: 0.5751 (t0) REVERT: A 552 MET cc_start: 0.8944 (mmp) cc_final: 0.8673 (mmp) REVERT: A 573 TYR cc_start: 0.7244 (t80) cc_final: 0.6645 (t80) REVERT: A 578 ASP cc_start: 0.7609 (t70) cc_final: 0.7298 (m-30) REVERT: A 604 ASN cc_start: 0.8046 (t0) cc_final: 0.7730 (t0) REVERT: A 686 TYR cc_start: 0.7870 (t80) cc_final: 0.7531 (t80) REVERT: D 3 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6936 (tt) REVERT: D 31 ASP cc_start: 0.6991 (t0) cc_final: 0.6696 (t0) REVERT: D 55 LYS cc_start: 0.8640 (mptt) cc_final: 0.8341 (mptt) REVERT: D 63 LEU cc_start: 0.7617 (pt) cc_final: 0.7038 (tt) REVERT: D 70 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8229 (ttp80) REVERT: D 91 GLN cc_start: 0.7404 (mp10) cc_final: 0.7204 (mt0) REVERT: C 87 ILE cc_start: 0.8761 (pt) cc_final: 0.8514 (pt) REVERT: C 110 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.7959 (mtt90) REVERT: G 67 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8285 (mtpp) REVERT: G 103 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8659 (tp) REVERT: G 176 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8597 (tt) REVERT: F 74 ASP cc_start: 0.8619 (t70) cc_final: 0.8150 (t70) REVERT: F 143 ARG cc_start: 0.8226 (ttt90) cc_final: 0.7981 (ttt90) REVERT: E 9 SER cc_start: 0.8520 (m) cc_final: 0.8267 (t) REVERT: B 17 SER cc_start: 0.8761 (m) cc_final: 0.8445 (t) REVERT: H 12 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8796 (tm) REVERT: H 22 ASN cc_start: 0.8534 (t0) cc_final: 0.8106 (t0) REVERT: H 83 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7676 (mmm160) REVERT: H 336 VAL cc_start: 0.8671 (m) cc_final: 0.8338 (t) outliers start: 79 outliers final: 41 residues processed: 387 average time/residue: 0.1617 time to fit residues: 94.2553 Evaluate side-chains 326 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 339 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 124 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 0.0770 chunk 197 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 42 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 134 ASN F 159 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.107381 restraints weight = 35981.114| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.20 r_work: 0.3281 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19867 Z= 0.194 Angle : 0.843 15.170 27139 Z= 0.398 Chirality : 0.065 1.144 3062 Planarity : 0.004 0.049 3243 Dihedral : 12.858 172.148 3276 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.01 % Favored : 90.95 % Rotamer: Outliers : 4.90 % Allowed : 16.09 % Favored : 79.01 % 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: -3.33 (0.16), residues: 2232 helix: -1.31 (0.17), residues: 823 sheet: -2.52 (0.27), residues: 317 loop : -2.85 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 81 TYR 0.024 0.002 TYR A 275 PHE 0.019 0.002 PHE A 655 TRP 0.020 0.002 TRP A 732 HIS 0.015 0.001 HIS H 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (19860) covalent geometry : angle 0.84168 / 0.40 (27133) hydrogen bonds : bond 0.04042 / 2.75 ( 624) hydrogen bonds : angle 4.93624 / 3.47 ( 1732) metal coordination : bond 0.00452 / 0.23 ( 4) metal coordination : angle 3.55284 / 1.73 ( 6) Misc. bond : bond 0.00150 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 308 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.7098 (m-80) cc_final: 0.6778 (m-80) REVERT: A 130 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6851 (mm) REVERT: A 202 SER cc_start: 0.8588 (m) cc_final: 0.8340 (p) REVERT: A 205 THR cc_start: 0.8877 (m) cc_final: 0.8539 (p) REVERT: A 235 PHE cc_start: 0.7520 (t80) cc_final: 0.7184 (t80) REVERT: A 276 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8746 (mp) REVERT: A 281 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7655 (mm-30) REVERT: A 285 ASP cc_start: 0.6859 (m-30) cc_final: 0.6414 (m-30) REVERT: A 300 TYR cc_start: 0.7609 (t80) cc_final: 0.7311 (t80) REVERT: A 373 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8040 (ttt) REVERT: A 384 TYR cc_start: 0.8056 (t80) cc_final: 0.7305 (t80) REVERT: A 415 ASP cc_start: 0.6795 (p0) cc_final: 0.5806 (t0) REVERT: A 573 TYR cc_start: 0.7257 (t80) cc_final: 0.6626 (t80) REVERT: A 578 ASP cc_start: 0.7671 (t70) cc_final: 0.7401 (m-30) REVERT: A 604 ASN cc_start: 0.8176 (t0) cc_final: 0.7724 (t0) REVERT: A 686 TYR cc_start: 0.7971 (t80) cc_final: 0.7632 (t80) REVERT: D 55 LYS cc_start: 0.8654 (mptt) cc_final: 0.8345 (mptt) REVERT: D 59 TYR cc_start: 0.8174 (t80) cc_final: 0.7831 (t80) REVERT: C 87 ILE cc_start: 0.8740 (pt) cc_final: 0.8496 (pt) REVERT: C 110 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.7937 (mtm110) REVERT: G 67 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8276 (mtpp) REVERT: G 137 GLN cc_start: 0.8350 (mt0) cc_final: 0.8009 (mm-40) REVERT: G 176 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8583 (tt) REVERT: F 74 ASP cc_start: 0.8657 (t70) cc_final: 0.8175 (t0) REVERT: F 165 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: E 9 SER cc_start: 0.8549 (m) cc_final: 0.8112 (p) REVERT: B 17 SER cc_start: 0.8775 (m) cc_final: 0.8485 (t) REVERT: B 286 VAL cc_start: 0.8317 (t) cc_final: 0.8017 (t) REVERT: H 12 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8781 (tm) REVERT: H 83 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7663 (mmm160) REVERT: H 345 MET cc_start: 0.8820 (tpp) cc_final: 0.8501 (tpp) outliers start: 91 outliers final: 50 residues processed: 370 average time/residue: 0.1529 time to fit residues: 85.7590 Evaluate side-chains 339 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 282 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 114 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 112 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN D 42 ASN D 76 GLN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102102 restraints weight = 36177.701| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.15 r_work: 0.3184 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 19867 Z= 0.340 Angle : 0.946 15.709 27139 Z= 0.449 Chirality : 0.070 0.736 3062 Planarity : 0.005 0.057 3243 Dihedral : 13.213 167.964 3276 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.89 % Favored : 89.07 % Rotamer: Outliers : 5.17 % Allowed : 17.06 % Favored : 77.77 % 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: -3.28 (0.16), residues: 2232 helix: -1.22 (0.17), residues: 817 sheet: -2.58 (0.27), residues: 308 loop : -2.84 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 338 TYR 0.023 0.002 TYR A 275 PHE 0.027 0.002 PHE B 64 TRP 0.024 0.003 TRP A 732 HIS 0.005 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.34 (19860) covalent geometry : angle 0.94469 / 0.45 (27133) hydrogen bonds : bond 0.04434 / 3.03 ( 624) hydrogen bonds : angle 5.13213 / 3.60 ( 1732) metal coordination : bond 0.00759 / 0.38 ( 4) metal coordination : angle 4.01582 / 2.01 ( 6) Misc. bond : bond 0.00145 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 271 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 SER cc_start: 0.8730 (m) cc_final: 0.8523 (p) REVERT: A 205 THR cc_start: 0.8955 (m) cc_final: 0.8597 (p) REVERT: A 235 PHE cc_start: 0.7512 (t80) cc_final: 0.7133 (t80) REVERT: A 276 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8794 (mp) REVERT: A 281 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 285 ASP cc_start: 0.6432 (m-30) cc_final: 0.5898 (m-30) REVERT: A 300 TYR cc_start: 0.7668 (t80) cc_final: 0.7432 (t80) REVERT: A 373 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8054 (ttt) REVERT: A 578 ASP cc_start: 0.7833 (t70) cc_final: 0.7440 (m-30) REVERT: A 604 ASN cc_start: 0.8255 (t0) cc_final: 0.7788 (t0) REVERT: A 686 TYR cc_start: 0.8254 (t80) cc_final: 0.8011 (t80) REVERT: D 22 ARG cc_start: 0.7992 (mmm-85) cc_final: 0.7574 (mmm-85) REVERT: D 31 ASP cc_start: 0.7277 (t0) cc_final: 0.6945 (t0) REVERT: D 55 LYS cc_start: 0.8697 (mptt) cc_final: 0.8286 (mptt) REVERT: D 59 TYR cc_start: 0.8339 (t80) cc_final: 0.8104 (t80) REVERT: C 87 ILE cc_start: 0.9015 (pt) cc_final: 0.8807 (pt) REVERT: C 110 ARG cc_start: 0.8610 (mtm-85) cc_final: 0.8347 (mtm-85) REVERT: G 67 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8334 (mtpp) REVERT: F 143 ARG cc_start: 0.8370 (ttt90) cc_final: 0.7978 (ttt90) REVERT: F 165 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7504 (pp20) REVERT: E 9 SER cc_start: 0.8654 (m) cc_final: 0.8286 (p) REVERT: E 130 THR cc_start: 0.8531 (m) cc_final: 0.8277 (p) REVERT: B 17 SER cc_start: 0.8895 (m) cc_final: 0.8673 (t) REVERT: B 98 LYS cc_start: 0.8558 (tttt) cc_final: 0.8303 (tptp) REVERT: B 286 VAL cc_start: 0.8438 (t) cc_final: 0.8169 (t) REVERT: H 12 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8771 (tm) REVERT: H 83 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7623 (mmm160) REVERT: H 336 VAL cc_start: 0.8761 (m) cc_final: 0.8414 (t) outliers start: 96 outliers final: 64 residues processed: 341 average time/residue: 0.1530 time to fit residues: 79.5730 Evaluate side-chains 317 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 248 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 97 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 149 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 661 ASN D 42 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106195 restraints weight = 35951.286| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.16 r_work: 0.3250 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19867 Z= 0.182 Angle : 0.817 14.992 27139 Z= 0.386 Chirality : 0.061 0.573 3062 Planarity : 0.004 0.052 3243 Dihedral : 13.118 172.373 3276 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.18 % Favored : 90.77 % Rotamer: Outliers : 4.41 % Allowed : 19.05 % Favored : 76.53 % 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: -2.98 (0.17), residues: 2232 helix: -0.85 (0.18), residues: 813 sheet: -2.52 (0.27), residues: 311 loop : -2.72 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 657 TYR 0.024 0.002 TYR A 275 PHE 0.018 0.002 PHE A 655 TRP 0.019 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (19860) covalent geometry : angle 0.81558 / 0.39 (27133) hydrogen bonds : bond 0.03940 / 2.69 ( 624) hydrogen bonds : angle 4.85122 / 3.41 ( 1732) metal coordination : bond 0.00391 / 0.20 ( 4) metal coordination : angle 3.24448 / 1.56 ( 6) Misc. bond : bond 0.00135 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 288 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 SER cc_start: 0.8706 (m) cc_final: 0.8472 (p) REVERT: A 205 THR cc_start: 0.8920 (m) cc_final: 0.8606 (p) REVERT: A 235 PHE cc_start: 0.7272 (t80) cc_final: 0.6960 (t80) REVERT: A 276 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 281 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 285 ASP cc_start: 0.6619 (m-30) cc_final: 0.6064 (m-30) REVERT: A 365 GLN cc_start: 0.8315 (mp-120) cc_final: 0.7994 (mp10) REVERT: A 373 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8009 (ttt) REVERT: A 552 MET cc_start: 0.9002 (mmp) cc_final: 0.8730 (mmp) REVERT: A 573 TYR cc_start: 0.7309 (t80) cc_final: 0.6767 (t80) REVERT: A 578 ASP cc_start: 0.7733 (t70) cc_final: 0.7488 (m-30) REVERT: A 604 ASN cc_start: 0.8194 (t0) cc_final: 0.7687 (t0) REVERT: A 657 ARG cc_start: 0.7825 (ttp80) cc_final: 0.6590 (ttp-170) REVERT: A 686 TYR cc_start: 0.8110 (t80) cc_final: 0.7861 (t80) REVERT: D 4 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8661 (pp) REVERT: D 55 LYS cc_start: 0.8646 (mptt) cc_final: 0.8239 (mptt) REVERT: C 87 ILE cc_start: 0.8822 (pt) cc_final: 0.8584 (pt) REVERT: C 110 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.8064 (mtm110) REVERT: G 67 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8299 (mtpp) REVERT: G 146 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8597 (t) REVERT: F 74 ASP cc_start: 0.8586 (t70) cc_final: 0.8190 (t0) REVERT: F 143 ARG cc_start: 0.8281 (ttt90) cc_final: 0.8032 (ttt90) REVERT: F 165 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7502 (pp20) REVERT: E 9 SER cc_start: 0.8500 (m) cc_final: 0.8092 (p) REVERT: E 130 THR cc_start: 0.8487 (m) cc_final: 0.8263 (p) REVERT: B 17 SER cc_start: 0.8764 (m) cc_final: 0.8517 (t) REVERT: B 98 LYS cc_start: 0.8518 (tttt) cc_final: 0.8293 (tptp) REVERT: B 286 VAL cc_start: 0.8304 (t) cc_final: 0.8096 (t) REVERT: H 12 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8828 (tm) REVERT: H 83 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7585 (mmm160) outliers start: 82 outliers final: 53 residues processed: 346 average time/residue: 0.1520 time to fit residues: 80.1474 Evaluate side-chains 318 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 258 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 213 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 504 ASN D 42 ASN G 159 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** 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 = 0.3720 r_free = 0.3720 target = 0.128210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108309 restraints weight = 36240.977| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.17 r_work: 0.3284 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19867 Z= 0.153 Angle : 0.787 14.516 27139 Z= 0.371 Chirality : 0.059 0.544 3062 Planarity : 0.004 0.051 3243 Dihedral : 12.925 173.619 3276 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.54 % Favored : 90.41 % Rotamer: Outliers : 4.20 % Allowed : 19.86 % Favored : 75.94 % 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: -2.77 (0.17), residues: 2232 helix: -0.57 (0.18), residues: 816 sheet: -2.31 (0.26), residues: 339 loop : -2.71 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 119 TYR 0.031 0.002 TYR B 157 PHE 0.025 0.001 PHE B 64 TRP 0.015 0.002 TRP A 732 HIS 0.008 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (19860) covalent geometry : angle 0.78558 / 0.37 (27133) hydrogen bonds : bond 0.03821 / 2.61 ( 624) hydrogen bonds : angle 4.71667 / 3.33 ( 1732) metal coordination : bond 0.00338 / 0.17 ( 4) metal coordination : angle 3.60874 / 1.87 ( 6) Misc. bond : bond 0.00130 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 295 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 SER cc_start: 0.8689 (m) cc_final: 0.8455 (p) REVERT: A 205 THR cc_start: 0.8879 (m) cc_final: 0.8582 (p) REVERT: A 235 PHE cc_start: 0.7168 (t80) cc_final: 0.6891 (t80) REVERT: A 237 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6656 (mm-30) REVERT: A 276 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8781 (mp) REVERT: A 281 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 285 ASP cc_start: 0.6673 (m-30) cc_final: 0.6037 (m-30) REVERT: A 373 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8005 (ttt) REVERT: A 573 TYR cc_start: 0.7288 (t80) cc_final: 0.6699 (t80) REVERT: A 578 ASP cc_start: 0.7735 (t70) cc_final: 0.7490 (m-30) REVERT: A 604 ASN cc_start: 0.8193 (t0) cc_final: 0.7706 (t0) REVERT: A 686 TYR cc_start: 0.8027 (t80) cc_final: 0.7773 (t80) REVERT: D 22 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7637 (mmm-85) REVERT: C 87 ILE cc_start: 0.8727 (pt) cc_final: 0.8488 (pt) REVERT: C 103 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7738 (tm-30) REVERT: C 110 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.7943 (mtm110) REVERT: G 67 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8265 (mtpp) REVERT: G 146 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8511 (t) REVERT: F 74 ASP cc_start: 0.8551 (t70) cc_final: 0.8163 (t0) REVERT: F 165 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: E 9 SER cc_start: 0.8468 (m) cc_final: 0.8067 (p) REVERT: E 130 THR cc_start: 0.8513 (m) cc_final: 0.8298 (p) REVERT: B 6 TYR cc_start: 0.8036 (m-10) cc_final: 0.7143 (m-10) REVERT: B 17 SER cc_start: 0.8702 (m) cc_final: 0.8344 (t) REVERT: B 47 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8280 (t0) REVERT: H 12 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8791 (tm) REVERT: H 50 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7338 (mtp) REVERT: H 83 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7572 (mmm160) outliers start: 78 outliers final: 51 residues processed: 352 average time/residue: 0.1584 time to fit residues: 84.4579 Evaluate side-chains 326 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 267 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 83 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 153 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 42 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108388 restraints weight = 36113.191| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.04 r_work: 0.3291 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19867 Z= 0.167 Angle : 0.802 14.289 27139 Z= 0.376 Chirality : 0.060 0.545 3062 Planarity : 0.004 0.050 3243 Dihedral : 12.860 172.963 3276 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.59 % Rotamer: Outliers : 3.98 % Allowed : 20.51 % Favored : 75.51 % 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: -2.62 (0.17), residues: 2232 helix: -0.40 (0.18), residues: 812 sheet: -2.21 (0.27), residues: 341 loop : -2.68 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 338 TYR 0.044 0.002 TYR B 157 PHE 0.018 0.001 PHE B 64 TRP 0.016 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (19860) covalent geometry : angle 0.80074 / 0.38 (27133) hydrogen bonds : bond 0.03838 / 2.61 ( 624) hydrogen bonds : angle 4.69027 / 3.30 ( 1732) metal coordination : bond 0.00408 / 0.20 ( 4) metal coordination : angle 3.62037 / 1.87 ( 6) Misc. bond : bond 0.00110 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 285 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 SER cc_start: 0.8723 (m) cc_final: 0.8438 (p) REVERT: A 205 THR cc_start: 0.8906 (m) cc_final: 0.8603 (p) REVERT: A 235 PHE cc_start: 0.7144 (t80) cc_final: 0.6918 (t80) REVERT: A 241 PHE cc_start: 0.7803 (m-80) cc_final: 0.7473 (m-80) REVERT: A 276 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8778 (mp) REVERT: A 281 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 285 ASP cc_start: 0.6397 (m-30) cc_final: 0.5211 (m-30) REVERT: A 373 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7997 (ttt) REVERT: A 552 MET cc_start: 0.8961 (mmp) cc_final: 0.8688 (mmp) REVERT: A 573 TYR cc_start: 0.7267 (t80) cc_final: 0.6580 (t80) REVERT: A 604 ASN cc_start: 0.8217 (t0) cc_final: 0.7710 (t0) REVERT: A 686 TYR cc_start: 0.8017 (t80) cc_final: 0.7768 (t80) REVERT: D 3 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6956 (tt) REVERT: D 22 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7684 (mmm-85) REVERT: C 80 GLU cc_start: 0.7230 (tp30) cc_final: 0.7003 (tp30) REVERT: C 87 ILE cc_start: 0.8751 (pt) cc_final: 0.8501 (pt) REVERT: C 110 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.7962 (mtm110) REVERT: G 67 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8281 (mtpp) REVERT: G 138 ILE cc_start: 0.9199 (pt) cc_final: 0.8979 (pt) REVERT: G 146 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8528 (t) REVERT: F 74 ASP cc_start: 0.8518 (t70) cc_final: 0.8126 (t0) REVERT: F 143 ARG cc_start: 0.8292 (ttt90) cc_final: 0.7766 (ttt90) REVERT: F 165 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7547 (pp20) REVERT: E 9 SER cc_start: 0.8496 (m) cc_final: 0.8105 (p) REVERT: E 130 THR cc_start: 0.8508 (m) cc_final: 0.8307 (p) REVERT: B 6 TYR cc_start: 0.7992 (m-10) cc_final: 0.7041 (m-10) REVERT: B 17 SER cc_start: 0.8666 (m) cc_final: 0.8333 (t) REVERT: B 47 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8305 (t0) REVERT: H 12 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8775 (tm) REVERT: H 50 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7375 (mtp) REVERT: H 71 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7905 (ttm110) outliers start: 74 outliers final: 53 residues processed: 337 average time/residue: 0.1536 time to fit residues: 78.9965 Evaluate side-chains 330 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 44 optimal weight: 0.0000 chunk 180 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 chunk 137 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN D 42 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106823 restraints weight = 35830.240| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.10 r_work: 0.3279 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19867 Z= 0.190 Angle : 0.823 14.314 27139 Z= 0.387 Chirality : 0.061 0.566 3062 Planarity : 0.004 0.049 3243 Dihedral : 12.869 172.122 3272 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.95 % Favored : 90.01 % Rotamer: Outliers : 3.71 % Allowed : 21.04 % Favored : 75.24 % 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: -2.56 (0.17), residues: 2232 helix: -0.30 (0.18), residues: 813 sheet: -2.21 (0.27), residues: 340 loop : -2.67 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 338 TYR 0.054 0.002 TYR B 157 PHE 0.018 0.002 PHE A 177 TRP 0.018 0.002 TRP A 732 HIS 0.005 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (19860) covalent geometry : angle 0.82120 / 0.39 (27133) hydrogen bonds : bond 0.03893 / 2.65 ( 624) hydrogen bonds : angle 4.73623 / 3.34 ( 1732) metal coordination : bond 0.00436 / 0.22 ( 4) metal coordination : angle 3.54055 / 1.84 ( 6) Misc. bond : bond 0.00121 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 271 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7566 (t60) cc_final: 0.6813 (t60) REVERT: A 202 SER cc_start: 0.8774 (m) cc_final: 0.8514 (p) REVERT: A 205 THR cc_start: 0.8939 (m) cc_final: 0.8631 (p) REVERT: A 276 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8798 (mp) REVERT: A 373 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8106 (ttt) REVERT: A 490 TYR cc_start: 0.7414 (t80) cc_final: 0.7204 (t80) REVERT: A 552 MET cc_start: 0.9030 (mmp) cc_final: 0.8780 (mmp) REVERT: A 573 TYR cc_start: 0.7492 (t80) cc_final: 0.6832 (t80) REVERT: A 604 ASN cc_start: 0.8270 (t0) cc_final: 0.7789 (t0) REVERT: A 686 TYR cc_start: 0.8270 (t80) cc_final: 0.8020 (t80) REVERT: D 3 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7075 (tt) REVERT: D 22 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7819 (mmm-85) REVERT: C 80 GLU cc_start: 0.7403 (tp30) cc_final: 0.7129 (tp30) REVERT: C 87 ILE cc_start: 0.8853 (pt) cc_final: 0.8622 (pt) REVERT: C 110 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8112 (mtm110) REVERT: G 67 LYS cc_start: 0.8673 (mmtt) cc_final: 0.8328 (mtpp) REVERT: G 146 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8591 (t) REVERT: F 74 ASP cc_start: 0.8759 (t70) cc_final: 0.8318 (t0) REVERT: F 143 ARG cc_start: 0.8344 (ttt90) cc_final: 0.7878 (ttt90) REVERT: F 165 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7693 (pp20) REVERT: F 180 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: E 9 SER cc_start: 0.8610 (m) cc_final: 0.8227 (p) REVERT: B 17 SER cc_start: 0.8759 (m) cc_final: 0.8450 (t) REVERT: B 47 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8433 (t0) REVERT: H 12 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8805 (tm) REVERT: H 50 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7510 (mtp) REVERT: H 178 ASP cc_start: 0.7995 (p0) cc_final: 0.7758 (p0) outliers start: 69 outliers final: 55 residues processed: 316 average time/residue: 0.1487 time to fit residues: 72.4471 Evaluate side-chains 328 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 264 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 108 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 211 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 42 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112442 restraints weight = 35988.554| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.02 r_work: 0.3357 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19867 Z= 0.130 Angle : 0.773 13.279 27139 Z= 0.363 Chirality : 0.057 0.490 3062 Planarity : 0.004 0.046 3243 Dihedral : 12.692 175.317 3272 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.56 % Favored : 91.40 % Rotamer: Outliers : 2.91 % Allowed : 22.01 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.17), residues: 2232 helix: -0.07 (0.18), residues: 811 sheet: -2.13 (0.27), residues: 345 loop : -2.63 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 338 TYR 0.069 0.002 TYR B 157 PHE 0.014 0.001 PHE A 241 TRP 0.011 0.002 TRP A 732 HIS 0.005 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (19860) covalent geometry : angle 0.77158 / 0.36 (27133) hydrogen bonds : bond 0.03800 / 2.59 ( 624) hydrogen bonds : angle 4.59420 / 3.24 ( 1732) metal coordination : bond 0.00223 / 0.11 ( 4) metal coordination : angle 3.52308 / 1.84 ( 6) Misc. bond : bond 0.00091 / 0.04 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 SER cc_start: 0.8608 (m) cc_final: 0.8306 (p) REVERT: A 205 THR cc_start: 0.8830 (m) cc_final: 0.8535 (p) REVERT: A 276 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 373 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7981 (ttt) REVERT: A 435 ASP cc_start: 0.7674 (t0) cc_final: 0.7452 (t0) REVERT: A 573 TYR cc_start: 0.7210 (t80) cc_final: 0.6489 (t80) REVERT: A 604 ASN cc_start: 0.8153 (t0) cc_final: 0.7671 (t0) REVERT: A 686 TYR cc_start: 0.7874 (t80) cc_final: 0.7637 (t80) REVERT: C 110 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8025 (mtm110) REVERT: G 67 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8282 (mtpp) REVERT: G 146 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8455 (t) REVERT: G 181 TYR cc_start: 0.8532 (p90) cc_final: 0.8196 (p90) REVERT: F 74 ASP cc_start: 0.8476 (t70) cc_final: 0.8110 (t70) REVERT: F 143 ARG cc_start: 0.8054 (ttt90) cc_final: 0.7787 (ttt90) REVERT: F 165 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7520 (pp20) REVERT: F 180 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: E 9 SER cc_start: 0.8353 (m) cc_final: 0.7953 (p) REVERT: B 6 TYR cc_start: 0.7778 (m-10) cc_final: 0.7036 (m-10) REVERT: B 17 SER cc_start: 0.8542 (m) cc_final: 0.8204 (t) REVERT: B 47 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8334 (t0) REVERT: B 91 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7985 (mptt) REVERT: H 12 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8787 (tm) REVERT: H 50 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7182 (mtp) REVERT: H 241 ARG cc_start: 0.7995 (mmp80) cc_final: 0.7749 (mmp80) outliers start: 54 outliers final: 36 residues processed: 333 average time/residue: 0.1563 time to fit residues: 79.5336 Evaluate side-chains 315 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 127 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 166 optimal weight: 0.1980 chunk 217 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 42 ASN G 144 ASN F 144 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.108747 restraints weight = 35900.671| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.08 r_work: 0.3305 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19867 Z= 0.179 Angle : 0.818 14.421 27139 Z= 0.385 Chirality : 0.060 0.534 3062 Planarity : 0.004 0.055 3243 Dihedral : 12.711 172.453 3272 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.81 % Favored : 90.14 % Rotamer: Outliers : 2.96 % Allowed : 22.12 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.17), residues: 2232 helix: -0.07 (0.19), residues: 812 sheet: -2.09 (0.27), residues: 341 loop : -2.61 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 338 TYR 0.062 0.002 TYR B 157 PHE 0.045 0.002 PHE B 64 TRP 0.017 0.002 TRP A 38 HIS 0.005 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (19860) covalent geometry : angle 0.81621 / 0.38 (27133) hydrogen bonds : bond 0.03831 / 2.61 ( 624) hydrogen bonds : angle 4.66630 / 3.29 ( 1732) metal coordination : bond 0.00483 / 0.24 ( 4) metal coordination : angle 3.54094 / 1.84 ( 6) Misc. bond : bond 0.00110 / 0.05 ( 3) =============================================================================== Job complete usr+sys time: 4339.24 seconds wall clock time: 75 minutes 30.19 seconds (4530.19 seconds total)