Starting phenix.real_space_refine on Thu Sep 18 18:20:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ig0_9660/09_2025/6ig0_9660.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ig0_9660/09_2025/6ig0_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2025/6ig0_9660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2025/6ig0_9660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2025/6ig0_9660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ig0_9660/09_2025/6ig0_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-2.0-5805/lib/python3.9/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: {'RNA': 34} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 715 Classifications: {'RNA': 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: 4.57, per 1000 atoms: 0.24 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: 1.85 Conformation dependent library (CDL) restraints added in 762.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.52 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: 3.34 Time building geometry restraints manager: 2.36 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: 26804 4.16 - 8.33: 285 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 - 32.35: 11682 32.35 - 64.69: 291 64.69 - 97.04: 35 97.04 - 129.39: 0 129.39 - 161.73: 3 Dihedral angle restraints: 12011 sinusoidal: 5403 harmonic: 6608 Sorted by residual: dihedral pdb=" O4' C N 8 " pdb=" C1' C N 8 " pdb=" N1 C N 8 " pdb=" C2 C N 8 " ideal model delta sinusoidal sigma weight residual -128.00 33.73 -161.73 1 1.70e+01 3.46e-03 6.48e+01 dihedral pdb=" O4' C N 14 " pdb=" C1' C N 14 " pdb=" N1 C N 14 " pdb=" C2 C N 14 " ideal model delta sinusoidal sigma weight residual -128.00 8.67 -136.67 1 1.70e+01 3.46e-03 5.74e+01 dihedral pdb=" CA ASN A 639 " pdb=" C ASN A 639 " pdb=" N GLU A 640 " pdb=" CA GLU A 640 " ideal model delta harmonic sigma weight residual 180.00 142.78 37.22 0 5.00e+00 4.00e-02 5.54e+01 ... (remaining 12008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2922 0.132 - 0.264: 123 0.264 - 0.396: 13 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.310 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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= 0.442 Angle : 1.208 33.042 27139 Z= 0.688 Chirality : 0.068 0.659 3062 Planarity : 0.006 0.070 3243 Dihedral : 14.281 161.733 7749 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 aren 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 covalent geometry : bond 0.00878 (19860) covalent geometry : angle 1.18304 (27133) hydrogen bonds : bond 0.28698 ( 624) hydrogen bonds : angle 10.42501 ( 1732) metal coordination : bond 0.11395 ( 4) metal coordination : angle 16.41979 ( 6) Misc. bond : bond 0.00376 ( 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 : 0.729 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: 0.6900 (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: 0.7543 (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: 0.6507 (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: 0.1837 time to fit residues: 165.4000 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 : 0.486 ------------------------------------------------------------------------------- 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: 0.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 135 ASN A 257 ASN A 639 ASN A 661 ASN A 735 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 284 HIS B 288 ASN H 154 ASN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 338 ASN H 339 HIS H 349 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109740 restraints weight = 35823.050| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.25 r_work: 0.3310 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19867 Z= 0.147 Angle : 0.732 14.180 27139 Z= 0.384 Chirality : 0.045 0.336 3062 Planarity : 0.005 0.056 3243 Dihedral : 15.220 162.838 3557 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.60 % Favored : 91.35 % Rotamer: Outliers : 3.82 % Allowed : 12.70 % Favored : 83.48 % 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 aren not related in a simple way. whole: -4.51 (0.14), residues: 2232 helix: -2.85 (0.13), residues: 823 sheet: -2.83 (0.26), residues: 318 loop : -3.13 (0.15), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 119 TYR 0.028 0.002 TYR C 59 PHE 0.028 0.002 PHE A 591 TRP 0.033 0.002 TRP A 732 HIS 0.005 0.001 HIS A 31 Details of bonding type rmsd covalent geometry : bond 0.00308 (19860) covalent geometry : angle 0.73021 (27133) hydrogen bonds : bond 0.04961 ( 624) hydrogen bonds : angle 5.75126 ( 1732) metal coordination : bond 0.00395 ( 4) metal coordination : angle 3.54589 ( 6) Misc. bond : bond 0.00209 ( 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 469 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 398 time to evaluate : 0.879 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: 0.7196 (m-80) cc_final: 0.6790 (m-80) REVERT: A 198 LEU cc_start: 0.8668 (tp) cc_final: 0.8412 (tp) REVERT: A 202 SER cc_start: 0.8569 (m) cc_final: 0.8320 (p) REVERT: A 205 THR cc_start: 0.8843 (m) cc_final: 0.8548 (p) REVERT: A 235 PHE cc_start: 0.7468 (t80) cc_final: 0.7211 (t80) REVERT: A 285 ASP cc_start: 0.7062 (m-30) cc_final: 0.6543 (m-30) REVERT: A 300 TYR cc_start: 0.7630 (t80) cc_final: 0.7111 (t80) REVERT: A 373 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8302 (ttt) REVERT: A 384 TYR cc_start: 0.7868 (t80) cc_final: 0.7558 (t80) REVERT: A 415 ASP cc_start: 0.6733 (p0) cc_final: 0.5786 (t0) REVERT: A 552 MET cc_start: 0.8968 (mmp) cc_final: 0.8706 (mmp) REVERT: A 578 ASP cc_start: 0.7563 (t70) cc_final: 0.7246 (m-30) REVERT: D 34 PHE cc_start: 0.8525 (m-10) cc_final: 0.8255 (m-80) REVERT: D 55 LYS cc_start: 0.8602 (mptt) cc_final: 0.8190 (mptt) REVERT: D 58 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7722 (mp0) REVERT: D 63 LEU cc_start: 0.7492 (pt) cc_final: 0.6771 (tt) REVERT: D 70 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8053 (ttp80) REVERT: D 85 ASP cc_start: 0.7368 (t70) cc_final: 0.7104 (t0) REVERT: C 21 GLU cc_start: 0.7325 (pm20) cc_final: 0.7057 (tp30) REVERT: C 87 ILE cc_start: 0.8710 (pt) cc_final: 0.8470 (pt) REVERT: C 102 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7122 (ttm-80) REVERT: G 67 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8280 (mtpp) REVERT: G 86 SER cc_start: 0.8397 (p) cc_final: 0.8190 (t) REVERT: G 103 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8715 (tp) REVERT: G 122 PHE cc_start: 0.8031 (m-80) cc_final: 0.7682 (m-80) REVERT: F 74 ASP cc_start: 0.8594 (t70) cc_final: 0.8183 (t70) REVERT: E 9 SER cc_start: 0.8476 (m) cc_final: 0.8129 (t) REVERT: E 39 ASP cc_start: 0.8601 (t0) cc_final: 0.8398 (t0) REVERT: E 167 PHE cc_start: 0.7612 (m-10) cc_final: 0.6944 (m-80) REVERT: E 168 LYS cc_start: 0.8479 (ttmm) cc_final: 0.8248 (tttm) REVERT: B 229 MET cc_start: 0.8469 (mmt) cc_final: 0.8192 (mmm) REVERT: B 231 ASP cc_start: 0.7233 (t0) cc_final: 0.7008 (t0) REVERT: B 238 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7859 (tptm) REVERT: H 12 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8756 (tm) REVERT: H 22 ASN cc_start: 0.8638 (t0) cc_final: 0.8282 (t0) REVERT: H 83 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7589 (mmm160) outliers start: 71 outliers final: 30 residues processed: 448 average time/residue: 0.1596 time to fit residues: 104.9840 Evaluate side-chains 333 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 33 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 373 MET 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 D residue 72 GLN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 103 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 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 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: 3.9990 chunk 89 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN G 85 ASN ** G 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107394 restraints weight = 35974.286| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.14 r_work: 0.3276 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3626 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= 0.177 Angle : 0.697 15.003 27139 Z= 0.362 Chirality : 0.045 0.323 3062 Planarity : 0.004 0.055 3243 Dihedral : 15.064 163.522 3541 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.14 % Favored : 90.82 % Rotamer: Outliers : 4.14 % Allowed : 15.66 % Favored : 80.19 % 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 aren not related in a simple way. whole: -3.68 (0.15), residues: 2232 helix: -1.81 (0.16), residues: 817 sheet: -2.60 (0.27), residues: 324 loop : -2.90 (0.16), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 94 TYR 0.022 0.002 TYR A 275 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 covalent geometry : bond 0.00393 (19860) covalent geometry : angle 0.69532 (27133) hydrogen bonds : bond 0.04148 ( 624) hydrogen bonds : angle 5.09251 ( 1732) metal coordination : bond 0.00365 ( 4) metal coordination : angle 3.14881 ( 6) Misc. bond : bond 0.00263 ( 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 404 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 327 time to evaluate : 0.775 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: A 54 TYR cc_start: 0.7263 (m-80) cc_final: 0.6880 (m-80) REVERT: A 130 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6850 (mm) REVERT: A 198 LEU cc_start: 0.8649 (tp) cc_final: 0.8402 (tp) REVERT: A 202 SER cc_start: 0.8580 (m) cc_final: 0.8332 (p) REVERT: A 205 THR cc_start: 0.8895 (m) cc_final: 0.8569 (p) REVERT: A 235 PHE cc_start: 0.7569 (t80) cc_final: 0.7338 (t80) REVERT: A 281 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 285 ASP cc_start: 0.6919 (m-30) cc_final: 0.6477 (m-30) REVERT: A 300 TYR cc_start: 0.7560 (t80) cc_final: 0.7158 (t80) REVERT: A 373 MET cc_start: 0.8623 (ttt) cc_final: 0.8277 (ttt) REVERT: A 384 TYR cc_start: 0.8088 (t80) cc_final: 0.7714 (t80) REVERT: A 460 LYS cc_start: 0.8661 (mptm) cc_final: 0.8435 (tptt) REVERT: A 521 ASP cc_start: 0.7978 (m-30) cc_final: 0.7731 (m-30) REVERT: A 552 MET cc_start: 0.8950 (mmp) cc_final: 0.8675 (mmp) REVERT: A 573 TYR cc_start: 0.7206 (t80) cc_final: 0.6808 (t80) REVERT: A 578 ASP cc_start: 0.7604 (t70) cc_final: 0.7326 (m-30) REVERT: D 37 THR cc_start: 0.8315 (m) cc_final: 0.8090 (p) REVERT: D 55 LYS cc_start: 0.8642 (mptt) cc_final: 0.8327 (mptt) REVERT: D 63 LEU cc_start: 0.7565 (pt) cc_final: 0.6977 (tt) REVERT: D 72 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7921 (pt0) REVERT: C 87 ILE cc_start: 0.8700 (pt) cc_final: 0.8436 (pt) REVERT: G 67 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8292 (mtpp) REVERT: G 103 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8726 (tp) REVERT: G 190 TYR cc_start: 0.8490 (m-80) cc_final: 0.8207 (m-10) REVERT: F 74 ASP cc_start: 0.8636 (t70) cc_final: 0.8210 (t70) REVERT: F 143 ARG cc_start: 0.8230 (ttt90) cc_final: 0.7997 (ttt90) REVERT: E 9 SER cc_start: 0.8524 (m) cc_final: 0.8240 (t) REVERT: B 113 ASP cc_start: 0.8210 (t0) cc_final: 0.8006 (t0) REVERT: H 12 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8771 (tm) REVERT: H 22 ASN cc_start: 0.8623 (t0) cc_final: 0.8234 (t0) REVERT: H 50 MET cc_start: 0.7491 (ttp) cc_final: 0.7273 (ttp) REVERT: H 83 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7650 (mmm160) REVERT: H 336 VAL cc_start: 0.8663 (m) cc_final: 0.8331 (t) outliers start: 77 outliers final: 42 residues processed: 384 average time/residue: 0.1735 time to fit residues: 98.4808 Evaluate side-chains 332 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 GLN 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 F residue 67 LYS 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 12 ILE 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 45 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 78 TYR 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 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 25 LYS 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 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 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: 1.9990 chunk 69 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS D 42 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN H 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106353 restraints weight = 35942.838| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.12 r_work: 0.3260 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3998 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= 0.178 Angle : 0.684 14.701 27139 Z= 0.354 Chirality : 0.044 0.322 3062 Planarity : 0.004 0.043 3243 Dihedral : 15.003 163.984 3538 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.05 % Favored : 90.91 % Rotamer: Outliers : 4.79 % Allowed : 15.88 % Favored : 79.33 % 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 aren not related in a simple way. whole: -3.20 (0.16), residues: 2232 helix: -1.22 (0.17), residues: 812 sheet: -2.49 (0.27), residues: 324 loop : -2.73 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 81 TYR 0.020 0.002 TYR A 275 PHE 0.019 0.002 PHE A 655 TRP 0.020 0.002 TRP A 732 HIS 0.021 0.001 HIS H 339 Details of bonding type rmsd covalent geometry : bond 0.00397 (19860) covalent geometry : angle 0.68247 (27133) hydrogen bonds : bond 0.03896 ( 624) hydrogen bonds : angle 4.89550 ( 1732) metal coordination : bond 0.00440 ( 4) metal coordination : angle 3.30822 ( 6) Misc. bond : bond 0.00227 ( 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 400 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 311 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.7132 (tm-30) cc_final: 0.6682 (tm-30) REVERT: A 54 TYR cc_start: 0.7111 (m-80) cc_final: 0.6742 (m-80) REVERT: A 130 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6938 (mm) REVERT: A 202 SER cc_start: 0.8593 (m) cc_final: 0.8356 (p) REVERT: A 205 THR cc_start: 0.8864 (m) cc_final: 0.8536 (p) REVERT: A 235 PHE cc_start: 0.7545 (t80) cc_final: 0.7243 (t80) REVERT: A 276 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 281 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 285 ASP cc_start: 0.6922 (m-30) cc_final: 0.6550 (m-30) REVERT: A 289 ASP cc_start: 0.7927 (p0) cc_final: 0.7526 (m-30) REVERT: A 300 TYR cc_start: 0.7574 (t80) cc_final: 0.7284 (t80) REVERT: A 373 MET cc_start: 0.8630 (ttt) cc_final: 0.8155 (ttt) REVERT: A 384 TYR cc_start: 0.8058 (t80) cc_final: 0.7741 (t80) REVERT: A 415 ASP cc_start: 0.6773 (p0) cc_final: 0.5820 (t0) REVERT: A 521 ASP cc_start: 0.8036 (m-30) cc_final: 0.7750 (m-30) REVERT: A 573 TYR cc_start: 0.7211 (t80) cc_final: 0.6790 (t80) REVERT: A 578 ASP cc_start: 0.7589 (t70) cc_final: 0.7335 (m-30) REVERT: A 604 ASN cc_start: 0.8072 (t0) cc_final: 0.7657 (t0) REVERT: D 3 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7016 (tt) REVERT: D 31 ASP cc_start: 0.7288 (t0) cc_final: 0.6988 (t0) REVERT: D 37 THR cc_start: 0.8389 (m) cc_final: 0.8182 (p) REVERT: D 55 LYS cc_start: 0.8622 (mptt) cc_final: 0.8328 (mptt) REVERT: D 63 LEU cc_start: 0.7502 (pt) cc_final: 0.7106 (tt) REVERT: D 70 ARG cc_start: 0.8513 (ttp80) cc_final: 0.7956 (ttp80) REVERT: D 72 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7920 (pt0) REVERT: C 87 ILE cc_start: 0.8744 (pt) cc_final: 0.8491 (pt) REVERT: G 67 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8284 (mtpp) REVERT: F 74 ASP cc_start: 0.8614 (t70) cc_final: 0.8163 (t70) REVERT: E 9 SER cc_start: 0.8553 (m) cc_final: 0.8104 (p) REVERT: B 47 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8256 (t0) REVERT: H 12 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8796 (tm) REVERT: H 22 ASN cc_start: 0.8618 (t0) cc_final: 0.8354 (t0) outliers start: 89 outliers final: 50 residues processed: 374 average time/residue: 0.1621 time to fit residues: 90.9575 Evaluate side-chains 338 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 86 SER 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 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 174 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 GLU 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 108 LEU 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 B residue 288 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 114 optimal weight: 0.6980 chunk 6 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN D 76 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN E 19 HIS E 33 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.124989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.104017 restraints weight = 36017.656| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.20 r_work: 0.3223 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19867 Z= 0.204 Angle : 0.694 14.849 27139 Z= 0.360 Chirality : 0.045 0.329 3062 Planarity : 0.004 0.045 3243 Dihedral : 14.996 164.347 3532 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.59 % Favored : 90.37 % Rotamer: Outliers : 4.79 % Allowed : 17.44 % 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 aren not related in a simple way. whole: -3.00 (0.17), residues: 2232 helix: -0.95 (0.17), residues: 824 sheet: -2.30 (0.27), residues: 332 loop : -2.74 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 81 TYR 0.018 0.002 TYR A 275 PHE 0.024 0.002 PHE B 64 TRP 0.020 0.002 TRP A 732 HIS 0.005 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00456 (19860) covalent geometry : angle 0.69260 (27133) hydrogen bonds : bond 0.03831 ( 624) hydrogen bonds : angle 4.83232 ( 1732) metal coordination : bond 0.00553 ( 4) metal coordination : angle 3.34018 ( 6) Misc. bond : bond 0.00203 ( 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 385 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 296 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.7092 (m-80) cc_final: 0.6740 (m-80) REVERT: A 130 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6972 (mm) REVERT: A 202 SER cc_start: 0.8676 (m) cc_final: 0.8469 (p) REVERT: A 205 THR cc_start: 0.8903 (m) cc_final: 0.8580 (p) REVERT: A 235 PHE cc_start: 0.7463 (t80) cc_final: 0.7126 (t80) REVERT: A 276 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8715 (mp) REVERT: A 281 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 285 ASP cc_start: 0.6917 (m-30) cc_final: 0.6492 (m-30) REVERT: A 289 ASP cc_start: 0.7953 (p0) cc_final: 0.7643 (m-30) REVERT: A 300 TYR cc_start: 0.7631 (t80) cc_final: 0.7368 (t80) REVERT: A 373 MET cc_start: 0.8593 (ttt) cc_final: 0.8018 (ttt) REVERT: A 384 TYR cc_start: 0.8078 (t80) cc_final: 0.7655 (t80) REVERT: A 521 ASP cc_start: 0.7985 (m-30) cc_final: 0.7714 (m-30) REVERT: A 578 ASP cc_start: 0.7762 (t70) cc_final: 0.7402 (m-30) REVERT: A 604 ASN cc_start: 0.8236 (t0) cc_final: 0.7728 (t0) REVERT: A 686 TYR cc_start: 0.8144 (t80) cc_final: 0.7870 (t80) REVERT: D 37 THR cc_start: 0.8505 (m) cc_final: 0.8298 (p) REVERT: D 55 LYS cc_start: 0.8644 (mptt) cc_final: 0.8340 (mptt) REVERT: D 93 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8254 (mt) REVERT: C 68 TYR cc_start: 0.8672 (t80) cc_final: 0.8428 (t80) REVERT: C 87 ILE cc_start: 0.8819 (pt) cc_final: 0.8579 (pt) REVERT: C 103 GLU cc_start: 0.7907 (mp0) cc_final: 0.7700 (tm-30) REVERT: G 67 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8286 (mtpp) REVERT: G 103 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8667 (tp) REVERT: F 74 ASP cc_start: 0.8599 (t70) cc_final: 0.8174 (t0) REVERT: F 143 ARG cc_start: 0.8258 (ttt180) cc_final: 0.7881 (ttt90) REVERT: E 9 SER cc_start: 0.8602 (m) cc_final: 0.8200 (p) REVERT: H 12 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8820 (tm) outliers start: 89 outliers final: 55 residues processed: 358 average time/residue: 0.1559 time to fit residues: 84.4459 Evaluate side-chains 332 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 379 ILE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 425 LEU 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 49 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 102 ARG 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 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 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 41 ILE 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 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 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 25 LYS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER 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: 9.9990 chunk 224 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 152 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN D 42 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 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 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102284 restraints weight = 36078.399| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.10 r_work: 0.3200 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19867 Z= 0.232 Angle : 0.710 15.046 27139 Z= 0.368 Chirality : 0.046 0.329 3062 Planarity : 0.004 0.042 3243 Dihedral : 15.027 163.047 3530 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.22 % Favored : 89.74 % Rotamer: Outliers : 4.63 % Allowed : 18.51 % Favored : 76.86 % 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 aren not related in a simple way. whole: -2.90 (0.17), residues: 2232 helix: -0.81 (0.18), residues: 817 sheet: -2.34 (0.27), residues: 330 loop : -2.69 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 81 TYR 0.034 0.002 TYR B 157 PHE 0.022 0.002 PHE A 655 TRP 0.021 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00521 (19860) covalent geometry : angle 0.70795 (27133) hydrogen bonds : bond 0.03909 ( 624) hydrogen bonds : angle 4.87262 ( 1732) metal coordination : bond 0.00625 ( 4) metal coordination : angle 3.66723 ( 6) Misc. bond : bond 0.00173 ( 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 379 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 293 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.7398 (tm-30) cc_final: 0.7096 (tm-30) REVERT: A 54 TYR cc_start: 0.7107 (m-80) cc_final: 0.6829 (m-80) REVERT: A 130 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7109 (mm) REVERT: A 202 SER cc_start: 0.8713 (m) cc_final: 0.8501 (p) REVERT: A 205 THR cc_start: 0.8943 (m) cc_final: 0.8626 (p) REVERT: A 235 PHE cc_start: 0.7352 (t80) cc_final: 0.6960 (t80) REVERT: A 276 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8758 (mp) REVERT: A 281 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 285 ASP cc_start: 0.6823 (m-30) cc_final: 0.6299 (m-30) REVERT: A 289 ASP cc_start: 0.7876 (p0) cc_final: 0.7664 (m-30) REVERT: A 300 TYR cc_start: 0.7626 (t80) cc_final: 0.7423 (t80) REVERT: A 373 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7951 (ttt) REVERT: A 384 TYR cc_start: 0.8143 (t80) cc_final: 0.7667 (t80) REVERT: A 521 ASP cc_start: 0.8019 (m-30) cc_final: 0.7721 (m-30) REVERT: A 573 TYR cc_start: 0.7236 (t80) cc_final: 0.6623 (t80) REVERT: A 604 ASN cc_start: 0.8267 (t0) cc_final: 0.7746 (t0) REVERT: A 657 ARG cc_start: 0.7847 (ttp80) cc_final: 0.6458 (ttp-170) REVERT: D 31 ASP cc_start: 0.7346 (t0) cc_final: 0.7134 (t0) REVERT: D 37 THR cc_start: 0.8478 (m) cc_final: 0.8266 (p) REVERT: D 55 LYS cc_start: 0.8657 (mptt) cc_final: 0.8391 (mttt) REVERT: D 72 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: D 93 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8242 (mt) REVERT: C 87 ILE cc_start: 0.8929 (pt) cc_final: 0.8728 (pt) REVERT: G 67 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8307 (mtpp) REVERT: F 74 ASP cc_start: 0.8560 (t70) cc_final: 0.8172 (t0) REVERT: F 143 ARG cc_start: 0.8280 (ttt180) cc_final: 0.8004 (ttt90) REVERT: E 9 SER cc_start: 0.8591 (m) cc_final: 0.8202 (p) REVERT: B 98 LYS cc_start: 0.8402 (tttt) cc_final: 0.8199 (tptp) REVERT: B 286 VAL cc_start: 0.8611 (t) cc_final: 0.8380 (t) REVERT: H 12 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8815 (tm) REVERT: H 50 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6917 (ttp) REVERT: H 345 MET cc_start: 0.8768 (tpp) cc_final: 0.8534 (tpp) outliers start: 86 outliers final: 62 residues processed: 355 average time/residue: 0.1440 time to fit residues: 77.6066 Evaluate side-chains 336 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 425 LEU 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 49 THR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 93 LEU 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 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 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 161 ASN 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 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 142 LEU Chi-restraints excluded: chain B residue 184 SER 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 25 LYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER 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 280 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: 0.8980 chunk 102 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 164 optimal weight: 0.0570 overall best weight: 2.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 661 ASN D 42 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN ** E 159 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105327 restraints weight = 36257.279| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.18 r_work: 0.3245 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19867 Z= 0.154 Angle : 0.665 14.580 27139 Z= 0.343 Chirality : 0.043 0.326 3062 Planarity : 0.004 0.033 3243 Dihedral : 14.954 165.116 3530 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.59 % Rotamer: Outliers : 3.77 % Allowed : 19.64 % Favored : 76.59 % 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 aren not related in a simple way. whole: -2.64 (0.17), residues: 2232 helix: -0.48 (0.18), residues: 805 sheet: -2.23 (0.27), residues: 334 loop : -2.62 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 119 TYR 0.041 0.002 TYR B 157 PHE 0.026 0.001 PHE B 64 TRP 0.017 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00340 (19860) covalent geometry : angle 0.66288 (27133) hydrogen bonds : bond 0.03672 ( 624) hydrogen bonds : angle 4.71433 ( 1732) metal coordination : bond 0.00401 ( 4) metal coordination : angle 3.27494 ( 6) Misc. bond : bond 0.00114 ( 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 380 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 310 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6982 (mm) REVERT: A 202 SER cc_start: 0.8672 (m) cc_final: 0.8442 (p) REVERT: A 205 THR cc_start: 0.8878 (m) cc_final: 0.8564 (p) REVERT: A 235 PHE cc_start: 0.7266 (t80) cc_final: 0.6985 (t80) REVERT: A 241 PHE cc_start: 0.7790 (m-80) cc_final: 0.7438 (m-80) REVERT: A 276 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8770 (mp) REVERT: A 281 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 285 ASP cc_start: 0.6907 (m-30) cc_final: 0.5860 (m-30) REVERT: A 289 ASP cc_start: 0.7944 (p0) cc_final: 0.7680 (m-30) REVERT: A 300 TYR cc_start: 0.7555 (t80) cc_final: 0.7345 (t80) REVERT: A 365 GLN cc_start: 0.8249 (mp-120) cc_final: 0.7969 (mp10) REVERT: A 373 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8008 (ttt) REVERT: A 521 ASP cc_start: 0.7971 (m-30) cc_final: 0.7739 (m-30) REVERT: A 573 TYR cc_start: 0.7271 (t80) cc_final: 0.6603 (t80) REVERT: A 604 ASN cc_start: 0.8221 (t0) cc_final: 0.7708 (t0) REVERT: D 37 THR cc_start: 0.8551 (m) cc_final: 0.8331 (p) REVERT: D 55 LYS cc_start: 0.8609 (mptt) cc_final: 0.8195 (mptt) REVERT: D 93 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8196 (mt) REVERT: C 87 ILE cc_start: 0.8841 (pt) cc_final: 0.8610 (pt) REVERT: G 67 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8257 (mtpp) REVERT: G 137 GLN cc_start: 0.8343 (mt0) cc_final: 0.7992 (mm-40) REVERT: F 74 ASP cc_start: 0.8513 (t70) cc_final: 0.8153 (t0) REVERT: F 143 ARG cc_start: 0.8231 (ttt180) cc_final: 0.8000 (ttt90) REVERT: E 9 SER cc_start: 0.8515 (m) cc_final: 0.8104 (p) REVERT: B 47 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8344 (t0) REVERT: B 98 LYS cc_start: 0.8394 (tttt) cc_final: 0.8183 (tptp) REVERT: H 12 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8804 (tm) outliers start: 70 outliers final: 41 residues processed: 360 average time/residue: 0.1565 time to fit residues: 83.7103 Evaluate side-chains 319 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 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 425 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain D residue 93 LEU 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 68 VAL 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 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 198 LEU 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 32 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER 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: 10.0000 chunk 41 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** E 159 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 = 0.3686 r_free = 0.3686 target = 0.125551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104877 restraints weight = 36210.956| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.12 r_work: 0.3241 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4780 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= 0.168 Angle : 0.679 14.290 27139 Z= 0.349 Chirality : 0.044 0.325 3062 Planarity : 0.004 0.040 3243 Dihedral : 14.926 166.568 3530 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.77 % Favored : 90.19 % Rotamer: Outliers : 3.44 % Allowed : 20.45 % Favored : 76.10 % 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 aren not related in a simple way. whole: -2.57 (0.17), residues: 2232 helix: -0.35 (0.18), residues: 806 sheet: -2.16 (0.27), residues: 344 loop : -2.65 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 119 TYR 0.049 0.002 TYR B 157 PHE 0.016 0.001 PHE B 64 TRP 0.017 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00373 (19860) covalent geometry : angle 0.67697 (27133) hydrogen bonds : bond 0.03698 ( 624) hydrogen bonds : angle 4.69574 ( 1732) metal coordination : bond 0.00475 ( 4) metal coordination : angle 3.73848 ( 6) Misc. bond : bond 0.00136 ( 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 352 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7083 (mm) REVERT: A 202 SER cc_start: 0.8719 (m) cc_final: 0.8473 (p) REVERT: A 205 THR cc_start: 0.8911 (m) cc_final: 0.8597 (p) REVERT: A 235 PHE cc_start: 0.7237 (t80) cc_final: 0.6935 (t80) REVERT: A 237 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6611 (mm-30) REVERT: A 276 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8775 (mp) REVERT: A 289 ASP cc_start: 0.7916 (p0) cc_final: 0.7689 (m-30) REVERT: A 300 TYR cc_start: 0.7571 (t80) cc_final: 0.7370 (t80) REVERT: A 365 GLN cc_start: 0.8228 (mp-120) cc_final: 0.7943 (mp10) REVERT: A 373 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7947 (ttt) REVERT: A 521 ASP cc_start: 0.8001 (m-30) cc_final: 0.7770 (m-30) REVERT: A 573 TYR cc_start: 0.7275 (t80) cc_final: 0.6582 (t80) REVERT: A 604 ASN cc_start: 0.8247 (t0) cc_final: 0.7720 (t0) REVERT: D 3 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.6933 (tt) REVERT: D 31 ASP cc_start: 0.7165 (t0) cc_final: 0.6943 (t0) REVERT: D 37 THR cc_start: 0.8470 (m) cc_final: 0.8267 (p) REVERT: D 93 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8193 (mt) REVERT: C 80 GLU cc_start: 0.7367 (tp30) cc_final: 0.7125 (tp30) REVERT: C 87 ILE cc_start: 0.8884 (pt) cc_final: 0.8648 (pt) REVERT: G 67 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8275 (mtpp) REVERT: G 137 GLN cc_start: 0.8294 (mt0) cc_final: 0.7937 (mm-40) REVERT: F 74 ASP cc_start: 0.8491 (t70) cc_final: 0.8139 (t0) REVERT: F 143 ARG cc_start: 0.8239 (ttt180) cc_final: 0.8028 (ttt90) REVERT: E 9 SER cc_start: 0.8507 (m) cc_final: 0.8125 (p) REVERT: B 47 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8322 (t0) REVERT: B 98 LYS cc_start: 0.8437 (tttt) cc_final: 0.8214 (tptp) REVERT: H 12 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8808 (tm) outliers start: 64 outliers final: 49 residues processed: 336 average time/residue: 0.1428 time to fit residues: 73.5152 Evaluate side-chains 333 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 425 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 506 ASN 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 A residue 746 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 93 LEU 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 68 VAL 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 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 198 LEU 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 32 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER 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: 9.9990 chunk 180 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 226 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** E 159 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 = 0.3668 r_free = 0.3668 target = 0.124340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103418 restraints weight = 35895.667| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.16 r_work: 0.3231 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4849 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= 0.191 Angle : 0.698 14.263 27139 Z= 0.359 Chirality : 0.045 0.327 3062 Planarity : 0.004 0.034 3243 Dihedral : 14.938 166.705 3530 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.13 % Favored : 89.83 % Rotamer: Outliers : 3.55 % Allowed : 20.45 % Favored : 76.00 % 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 aren not related in a simple way. whole: -2.55 (0.17), residues: 2232 helix: -0.30 (0.18), residues: 810 sheet: -2.15 (0.27), residues: 344 loop : -2.68 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 119 TYR 0.057 0.002 TYR B 157 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 covalent geometry : bond 0.00427 (19860) covalent geometry : angle 0.69553 (27133) hydrogen bonds : bond 0.03729 ( 624) hydrogen bonds : angle 4.72241 ( 1732) metal coordination : bond 0.00516 ( 4) metal coordination : angle 3.77375 ( 6) Misc. bond : bond 0.00173 ( 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 345 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 279 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7516 (t60) cc_final: 0.6821 (t60) REVERT: A 130 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7136 (mm) REVERT: A 202 SER cc_start: 0.8807 (m) cc_final: 0.8550 (p) REVERT: A 205 THR cc_start: 0.8927 (m) cc_final: 0.8616 (p) REVERT: A 235 PHE cc_start: 0.7218 (t80) cc_final: 0.6918 (t80) REVERT: A 237 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6712 (mm-30) REVERT: A 276 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 289 ASP cc_start: 0.8056 (p0) cc_final: 0.7740 (m-30) REVERT: A 365 GLN cc_start: 0.8231 (mp-120) cc_final: 0.7915 (mp10) REVERT: A 373 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8026 (ttt) REVERT: A 402 GLU cc_start: 0.7879 (tt0) cc_final: 0.7659 (tt0) REVERT: A 521 ASP cc_start: 0.8121 (m-30) cc_final: 0.7825 (m-30) REVERT: A 573 TYR cc_start: 0.7486 (t80) cc_final: 0.6813 (t80) REVERT: A 604 ASN cc_start: 0.8360 (t0) cc_final: 0.7838 (t0) REVERT: D 3 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7054 (tt) REVERT: D 37 THR cc_start: 0.8562 (m) cc_final: 0.8326 (p) REVERT: D 93 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8306 (mt) REVERT: C 80 GLU cc_start: 0.7583 (tp30) cc_final: 0.7335 (tp30) REVERT: C 87 ILE cc_start: 0.8941 (pt) cc_final: 0.8718 (pt) REVERT: G 67 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8307 (mtpp) REVERT: G 137 GLN cc_start: 0.8571 (mt0) cc_final: 0.8202 (mm-40) REVERT: F 74 ASP cc_start: 0.8728 (t70) cc_final: 0.8312 (t0) REVERT: E 9 SER cc_start: 0.8600 (m) cc_final: 0.8219 (p) REVERT: B 98 LYS cc_start: 0.8483 (tttt) cc_final: 0.8228 (tptp) REVERT: H 12 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8839 (tm) outliers start: 66 outliers final: 52 residues processed: 328 average time/residue: 0.1381 time to fit residues: 69.4330 Evaluate side-chains 325 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 425 LEU 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 A residue 618 ASP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 93 LEU 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 68 VAL 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 8 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 58 PHE 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 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 32 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 108 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN D 42 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** 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 = 0.3656 r_free = 0.3656 target = 0.123444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.103344 restraints weight = 35920.399| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.03 r_work: 0.3216 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.005 0.040 19867 Z= 0.215 Angle : 0.724 14.591 27139 Z= 0.371 Chirality : 0.045 0.332 3062 Planarity : 0.004 0.038 3243 Dihedral : 14.919 165.897 3530 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.71 % Favored : 89.25 % Rotamer: Outliers : 3.44 % Allowed : 20.83 % Favored : 75.73 % 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 aren not related in a simple way. whole: -2.57 (0.17), residues: 2232 helix: -0.31 (0.18), residues: 816 sheet: -2.15 (0.27), residues: 343 loop : -2.71 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 81 TYR 0.070 0.002 TYR B 157 PHE 0.019 0.002 PHE A 655 TRP 0.020 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00484 (19860) covalent geometry : angle 0.72163 (27133) hydrogen bonds : bond 0.03825 ( 624) hydrogen bonds : angle 4.79052 ( 1732) metal coordination : bond 0.00607 ( 4) metal coordination : angle 3.83047 ( 6) Misc. bond : bond 0.00152 ( 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 335 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 271 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7194 (mm) REVERT: A 202 SER cc_start: 0.8838 (m) cc_final: 0.8556 (p) REVERT: A 205 THR cc_start: 0.8946 (m) cc_final: 0.8620 (p) REVERT: A 235 PHE cc_start: 0.7237 (t80) cc_final: 0.6921 (t80) REVERT: A 276 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8761 (mp) REVERT: A 289 ASP cc_start: 0.8064 (p0) cc_final: 0.7773 (m-30) REVERT: A 365 GLN cc_start: 0.8273 (mp-120) cc_final: 0.7892 (mp10) REVERT: A 373 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8133 (ttt) REVERT: A 521 ASP cc_start: 0.8159 (m-30) cc_final: 0.7875 (m-30) REVERT: A 573 TYR cc_start: 0.7495 (t80) cc_final: 0.6910 (t80) REVERT: A 604 ASN cc_start: 0.8339 (t0) cc_final: 0.7840 (t0) REVERT: D 3 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7162 (tt) REVERT: D 37 THR cc_start: 0.8564 (m) cc_final: 0.8317 (p) REVERT: D 93 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 80 GLU cc_start: 0.7608 (tp30) cc_final: 0.7349 (tp30) REVERT: C 87 ILE cc_start: 0.8963 (pt) cc_final: 0.8748 (pt) REVERT: G 67 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8332 (mtpp) REVERT: G 137 GLN cc_start: 0.8631 (mt0) cc_final: 0.8237 (mm-40) REVERT: F 74 ASP cc_start: 0.8689 (t70) cc_final: 0.8270 (t0) REVERT: F 143 ARG cc_start: 0.8394 (ttt-90) cc_final: 0.8060 (ttt90) REVERT: E 9 SER cc_start: 0.8598 (m) cc_final: 0.8189 (p) REVERT: B 47 ASP cc_start: 0.8803 (m-30) cc_final: 0.8546 (t0) REVERT: B 98 LYS cc_start: 0.8457 (tttt) cc_final: 0.8238 (tptp) REVERT: H 12 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8868 (tm) REVERT: H 178 ASP cc_start: 0.8141 (p0) cc_final: 0.7906 (p0) outliers start: 64 outliers final: 57 residues processed: 318 average time/residue: 0.1383 time to fit residues: 67.4292 Evaluate side-chains 326 residues out of total 1954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 263 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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 425 LEU 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 A residue 618 ASP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 93 LEU 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 68 VAL 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 8 MET Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 78 TYR 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 B residue 282 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 127 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 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 = 0.3687 r_free = 0.3687 target = 0.125550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105223 restraints weight = 35854.054| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.12 r_work: 0.3244 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19867 Z= 0.169 Angle : 0.698 13.924 27139 Z= 0.357 Chirality : 0.044 0.330 3062 Planarity : 0.004 0.034 3243 Dihedral : 14.848 166.923 3530 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.63 % Favored : 90.32 % Rotamer: Outliers : 3.50 % Allowed : 20.88 % Favored : 75.62 % 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 aren not related in a simple way. whole: -2.48 (0.17), residues: 2232 helix: -0.25 (0.18), residues: 811 sheet: -2.12 (0.27), residues: 346 loop : -2.63 (0.17), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 119 TYR 0.075 0.002 TYR B 157 PHE 0.017 0.001 PHE A 348 TRP 0.018 0.002 TRP A 38 HIS 0.006 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00378 (19860) covalent geometry : angle 0.69486 (27133) hydrogen bonds : bond 0.03731 ( 624) hydrogen bonds : angle 4.71209 ( 1732) metal coordination : bond 0.00495 ( 4) metal coordination : angle 4.20144 ( 6) Misc. bond : bond 0.00137 ( 3) =============================================================================== Job complete usr+sys time: 4120.48 seconds wall clock time: 71 minutes 40.91 seconds (4300.91 seconds total)