Starting phenix.real_space_refine on Sun Sep 13 21:57:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eqg_31265/09_2026/7eqg_31265_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eqg_31265/09_2026/7eqg_31265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eqg_31265/09_2026/7eqg_31265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eqg_31265/09_2026/7eqg_31265.map" model { file = "/net/cci-nas-00/data/ceres_data/7eqg_31265/09_2026/7eqg_31265_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eqg_31265/09_2026/7eqg_31265_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians P 130 5.49 5 S 41 5.16 5 C 16072 2.51 5 N 4814 2.21 5 O 5244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26301 Number of models: 1 Model: "" Number of chains: 17 Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2360 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2516 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2544 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2548 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2560 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 566 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 571 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1429 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "M" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1226 Classifications: {'RNA': 58} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 19, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 32, 'rna3p': 25} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 907 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "P" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 568 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 570 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 567 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1893 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 17, 'TRANS': 245} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 7, 'HIS:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 131 Chain: "O" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 549 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {' DC:plan': 3, ' DC:plan2': 3, ' DA:plan': 1, ' DA:plan2': 1, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 5.36, per 1000 atoms: 0.20 Number of scatterers: 26301 At special positions: 0 Unit cell: (162.8, 136.4, 167.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 130 15.00 O 5244 8.00 N 4814 7.00 C 16072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5768 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 39 sheets defined 28.4% alpha, 18.3% beta 29 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'C' and resid 33 through 48 removed outlier: 4.090A pdb=" N PHE C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.591A pdb=" N GLN C 133 " --> pdb=" O GLN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 178 Processing helix chain 'C' and resid 189 through 201 removed outlier: 3.880A pdb=" N LEU C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.634A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.520A pdb=" N GLY D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 264 removed outlier: 3.549A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 removed outlier: 3.569A pdb=" N LEU D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.674A pdb=" N GLN D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.576A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 129 removed outlier: 3.672A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.601A pdb=" N ALA E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 removed outlier: 3.766A pdb=" N VAL E 153 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 205 removed outlier: 3.659A pdb=" N ALA E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 202 " --> pdb=" O LEU E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 266 removed outlier: 3.628A pdb=" N ILE E 260 " --> pdb=" O HIS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 314 removed outlier: 3.692A pdb=" N LEU E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.546A pdb=" N GLY E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 112 through 129 removed outlier: 3.679A pdb=" N GLN F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR F 125 " --> pdb=" O THR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 144 Processing helix chain 'F' and resid 189 through 205 removed outlier: 3.746A pdb=" N GLY F 202 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.701A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.799A pdb=" N LEU G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.849A pdb=" N LYS G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 144 removed outlier: 3.579A pdb=" N HIS G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 204 removed outlier: 3.751A pdb=" N GLU G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 266 removed outlier: 3.979A pdb=" N THR G 266 " --> pdb=" O ASN G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 278 removed outlier: 4.051A pdb=" N LEU G 277 " --> pdb=" O GLU G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 3.517A pdb=" N LEU G 313 " --> pdb=" O ASP G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 58 through 62 removed outlier: 4.177A pdb=" N ARG H 62 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 72 removed outlier: 4.394A pdb=" N ALA H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 129 Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 190 through 205 removed outlier: 3.728A pdb=" N ALA H 194 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU H 198 " --> pdb=" O ALA H 194 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 264 removed outlier: 3.562A pdb=" N ILE H 260 " --> pdb=" O HIS H 256 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU H 264 " --> pdb=" O ILE H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'I' and resid 63 through 72 removed outlier: 3.750A pdb=" N LEU I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN I 72 " --> pdb=" O ASP I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 129 Processing helix chain 'I' and resid 133 through 144 Processing helix chain 'I' and resid 190 through 204 Processing helix chain 'I' and resid 256 through 264 Processing helix chain 'I' and resid 274 through 278 removed outlier: 3.750A pdb=" N GLY I 278 " --> pdb=" O ASP I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 313 removed outlier: 3.648A pdb=" N LEU I 307 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 319 through 333 removed outlier: 3.874A pdb=" N TYR I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 53 Processing helix chain 'J' and resid 72 through 76 removed outlier: 3.968A pdb=" N ARG J 76 " --> pdb=" O GLU J 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 Processing helix chain 'L' and resid 16 through 34 removed outlier: 3.538A pdb=" N LEU L 20 " --> pdb=" O PRO L 16 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL L 23 " --> pdb=" O GLN L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 73 removed outlier: 3.566A pdb=" N ARG L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 77 removed outlier: 3.572A pdb=" N GLU L 77 " --> pdb=" O PRO L 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 74 through 77' Processing helix chain 'L' and resid 108 through 119 removed outlier: 3.910A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG L 119 " --> pdb=" O ARG L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 131 removed outlier: 3.535A pdb=" N LYS L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE L 131 " --> pdb=" O ALA L 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 54 Processing helix chain 'Q' and resid 39 through 55 Processing helix chain 'Q' and resid 72 through 77 removed outlier: 3.811A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL Q 77 " --> pdb=" O GLN Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 53 Processing helix chain 'B' and resid 13 through 33 removed outlier: 3.663A pdb=" N ILE B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 removed outlier: 3.897A pdb=" N THR B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 59 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.937A pdb=" N PHE B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 138 through 144 removed outlier: 3.833A pdb=" N VAL B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 162 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.172A pdb=" N ALA B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.545A pdb=" N ASN B 250 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 Processing sheet with id=AA1, first strand: chain 'C' and resid 56 through 61 removed outlier: 4.934A pdb=" N GLY C 58 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 112 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 110 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 56 through 61 removed outlier: 4.934A pdb=" N GLY C 58 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 112 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 110 " --> pdb=" O GLY C 60 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA C 103 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN C 18 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU C 105 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER C 16 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL C 107 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ARG C 14 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 109 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 12 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA4, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'C' and resid 185 through 188 Processing sheet with id=AA6, first strand: chain 'C' and resid 255 through 257 Processing sheet with id=AA7, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=AA8, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.826A pdb=" N GLY D 334 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.532A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 158 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP D 177 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL D 160 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG D 175 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE D 162 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR D 173 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.532A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 48 Processing sheet with id=AB3, first strand: chain 'E' and resid 108 through 109 removed outlier: 3.770A pdb=" N ALA E 108 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 20 removed outlier: 4.036A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE E 162 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AB6, first strand: chain 'E' and resid 44 through 51 removed outlier: 4.563A pdb=" N ALA E 82 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 12 through 14 removed outlier: 3.594A pdb=" N GLY F 334 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 170 through 177 removed outlier: 3.896A pdb=" N ARG F 172 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 94 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 24 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 44 through 51 Processing sheet with id=AC1, first strand: chain 'G' and resid 169 through 177 removed outlier: 5.038A pdb=" N VAL G 170 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ARG G 166 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 51 Processing sheet with id=AC3, first strand: chain 'H' and resid 13 through 14 removed outlier: 3.924A pdb=" N GLY H 334 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.978A pdb=" N VAL H 209 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG H 172 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AC6, first strand: chain 'H' and resid 45 through 48 removed outlier: 4.329A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 225 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 287 through 288 Processing sheet with id=AC8, first strand: chain 'I' and resid 108 through 109 removed outlier: 3.639A pdb=" N ALA I 108 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 19 through 20 removed outlier: 4.286A pdb=" N LEU I 210 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG I 172 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AD2, first strand: chain 'I' and resid 44 through 51 Processing sheet with id=AD3, first strand: chain 'I' and resid 266 through 268 Processing sheet with id=AD4, first strand: chain 'I' and resid 287 through 288 removed outlier: 3.892A pdb=" N LYS I 293 " --> pdb=" O VAL I 288 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 28 through 35 removed outlier: 5.125A pdb=" N MET J 29 " --> pdb=" O ARG J 25 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG J 25 " --> pdb=" O MET J 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG J 33 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL J 21 " --> pdb=" O ARG J 33 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG J 35 " --> pdb=" O TYR J 19 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR J 19 " --> pdb=" O ARG J 35 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR J 5 " --> pdb=" O VAL J 60 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU J 62 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL J 7 " --> pdb=" O LEU J 62 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 29 through 37 removed outlier: 3.565A pdb=" N VAL K 31 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL K 21 " --> pdb=" O ARG K 33 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ARG K 35 " --> pdb=" O TYR K 19 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR K 19 " --> pdb=" O ARG K 35 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 7 through 8 removed outlier: 3.544A pdb=" N LEU L 58 " --> pdb=" O ILE L 7 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 100 through 103 removed outlier: 4.213A pdb=" N PHE L 158 " --> pdb=" O VAL L 103 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 28 through 37 removed outlier: 5.713A pdb=" N VAL P 30 " --> pdb=" O ARG P 25 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ARG P 25 " --> pdb=" O VAL P 30 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY P 32 " --> pdb=" O VAL P 23 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL P 23 " --> pdb=" O GLY P 32 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR P 19 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR P 5 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU P 62 " --> pdb=" O THR P 5 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL P 7 " --> pdb=" O LEU P 62 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 28 through 35 removed outlier: 5.179A pdb=" N VAL Q 30 " --> pdb=" O ARG Q 25 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG Q 25 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLY Q 32 " --> pdb=" O VAL Q 23 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL Q 23 " --> pdb=" O GLY Q 32 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR Q 5 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU Q 62 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL Q 7 " --> pdb=" O LEU Q 62 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 31 through 35 removed outlier: 5.854A pdb=" N GLY R 32 " --> pdb=" O VAL R 23 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL R 23 " --> pdb=" O GLY R 32 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR R 5 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU R 62 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL R 7 " --> pdb=" O LEU R 62 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 180 through 181 859 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5292 1.33 - 1.45: 6733 1.45 - 1.57: 14713 1.57 - 1.69: 258 1.69 - 1.81: 74 Bond restraints: 27070 Sorted by residual: bond pdb=" C1' DT O 26 " pdb=" N1 DT O 26 " ideal model delta sigma weight residual 1.468 1.551 -0.083 1.40e-02 5.10e+03 3.52e+01 bond pdb=" C1' DC N 1 " pdb=" N1 DC N 1 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.94e+01 bond pdb=" C LEU C 263 " pdb=" N PRO C 264 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.08e-02 8.57e+03 1.45e+01 bond pdb=" N9 A M 12 " pdb=" C4 A M 12 " ideal model delta sigma weight residual 1.374 1.354 0.020 6.00e-03 2.78e+04 1.08e+01 bond pdb=" C1' DT N 17 " pdb=" N1 DT N 17 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.07e+01 ... (remaining 27065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 36243 2.23 - 4.46: 962 4.46 - 6.69: 88 6.69 - 8.92: 27 8.92 - 11.14: 7 Bond angle restraints: 37327 Sorted by residual: angle pdb=" C LEU B 268 " pdb=" N PRO B 269 " pdb=" CA PRO B 269 " ideal model delta sigma weight residual 119.66 126.39 -6.73 7.20e-01 1.93e+00 8.74e+01 angle pdb=" N LYS G 235 " pdb=" CA LYS G 235 " pdb=" C LYS G 235 " ideal model delta sigma weight residual 109.76 100.84 8.92 1.59e+00 3.96e-01 3.15e+01 angle pdb=" O5' C M 20 " pdb=" C5' C M 20 " pdb=" C4' C M 20 " ideal model delta sigma weight residual 109.40 113.87 -4.47 8.00e-01 1.56e+00 3.12e+01 angle pdb=" O5' G M 26 " pdb=" C5' G M 26 " pdb=" C4' G M 26 " ideal model delta sigma weight residual 109.40 113.82 -4.42 8.00e-01 1.56e+00 3.06e+01 angle pdb=" O5' G M 14 " pdb=" C5' G M 14 " pdb=" C4' G M 14 " ideal model delta sigma weight residual 109.40 113.67 -4.27 8.00e-01 1.56e+00 2.85e+01 ... (remaining 37322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 15432 35.90 - 71.79: 702 71.79 - 107.69: 55 107.69 - 143.59: 4 143.59 - 179.49: 7 Dihedral angle restraints: 16200 sinusoidal: 7256 harmonic: 8944 Sorted by residual: dihedral pdb=" O4' C M 49 " pdb=" C1' C M 49 " pdb=" N1 C M 49 " pdb=" C2 C M 49 " ideal model delta sinusoidal sigma weight residual 200.00 49.78 150.22 1 1.50e+01 4.44e-03 7.97e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual -128.00 49.49 -177.49 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual -128.00 45.45 -173.45 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 16197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4096 0.128 - 0.257: 138 0.257 - 0.385: 2 0.385 - 0.514: 0 0.514 - 0.642: 1 Chirality restraints: 4237 Sorted by residual: chirality pdb=" C3' G M 48 " pdb=" C4' G M 48 " pdb=" O3' G M 48 " pdb=" C2' G M 48 " both_signs ideal model delta sigma weight residual False -2.74 -2.10 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA LEU G 18 " pdb=" N LEU G 18 " pdb=" C LEU G 18 " pdb=" CB LEU G 18 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB THR E 266 " pdb=" CA THR E 266 " pdb=" OG1 THR E 266 " pdb=" CG2 THR E 266 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4234 not shown) Planarity restraints: 4453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 56 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO K 57 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO K 57 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 57 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 71 " -0.053 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO B 72 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 25 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO C 26 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 26 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 26 " 0.043 5.00e-02 4.00e+02 ... (remaining 4450 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 47 2.41 - 3.03: 13299 3.03 - 3.66: 36837 3.66 - 4.28: 55906 4.28 - 4.90: 96035 Nonbonded interactions: 202124 Sorted by model distance: nonbonded pdb=" N2 G M 48 " pdb=" N1 A M 55 " model vdw 1.791 2.560 nonbonded pdb=" O GLU L 110 " pdb=" CD ARG L 114 " model vdw 1.898 3.440 nonbonded pdb=" O2' U M 47 " pdb=" OP2 G M 48 " model vdw 1.957 3.040 nonbonded pdb=" NH2 ARG L 115 " pdb=" O2' G M 48 " model vdw 1.959 3.120 nonbonded pdb=" O ASN D 144 " pdb=" OD1 ASN D 144 " model vdw 2.062 3.040 ... (remaining 202119 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 'D' and (resid 6 through 32 or (resid 33 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 146 or (resid 147 throug \ h 152 and (name N or name CA or name C or name O or name CB )) or resid 153 thro \ ugh 236 or (resid 237 through 239 and (name N or name CA or name C or name O or \ name CB )) or resid 240 through 242 or (resid 243 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 272 or (resid 273 through 275 an \ d (name N or name CA or name C or name O or name CB )) or resid 276 through 300 \ or (resid 301 through 302 and (name N or name CA or name C or name O or name CB \ )) or resid 303 through 338)) selection = (chain 'E' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 46 or (resid 147 through 152 and (name N or name CA or name C or name O or name \ CB )) or resid 153 through 236 or (resid 237 through 239 and (name N or name CA \ or name C or name O or name CB )) or resid 240 through 242 or (resid 243 and (na \ me N or name CA or name C or name O or name CB )) or resid 244 through 338)) selection = (chain 'F' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 46 or (resid 147 through 152 and (name N or name CA or name C or name O or name \ CB )) or resid 153 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB )) or resid 185 through 236 or (resid 237 through 239 and (na \ me N or name CA or name C or name O or name CB )) or resid 240 through 272 or (r \ esid 273 through 275 and (name N or name CA or name C or name O or name CB )) or \ resid 276 or (resid 277 and (name N or name CA or name C or name O or name CB ) \ ) or resid 278 through 300 or (resid 301 through 302 and (name N or name CA or n \ ame C or name O or name CB )) or resid 303 through 338)) selection = (chain 'G' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 83 or (resid 184 and (name N or name CA or name C or name O or name CB )) or res \ id 185 through 237 or (resid 238 through 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 242 or (resid 243 and (name N or name \ CA or name C or name O or name CB )) or resid 244 through 271 or (resid 272 thr \ ough 275 and (name N or name CA or name C or name O or name CB )) or resid 276 t \ hrough 300 or (resid 301 through 302 and (name N or name CA or name C or name O \ or name CB )) or resid 303 through 338)) selection = (chain 'H' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 46 or (resid 147 through 152 and (name N or name CA or name C or name O or name \ CB )) or resid 153 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB )) or resid 185 through 236 or (resid 237 through 239 and (na \ me N or name CA or name C or name O or name CB )) or resid 240 through 242 or (r \ esid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 276 or (resid 277 and (name N or name CA or name C or name O or name CB ) \ ) or resid 278 through 300 or (resid 301 through 302 and (name N or name CA or n \ ame C or name O or name CB )) or resid 303 through 338)) selection = (chain 'I' and (resid 6 through 29 or (resid 30 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 49 or resid 76 through 1 \ 46 or (resid 147 through 152 and (name N or name CA or name C or name O or name \ CB )) or resid 153 through 183 or (resid 184 and (name N or name CA or name C or \ name O or name CB )) or resid 185 through 236 or (resid 237 through 239 and (na \ me N or name CA or name C or name O or name CB )) or resid 240 through 242 or (r \ esid 243 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 271 or (resid 272 through 275 and (name N or name CA or name C or name O \ or name CB )) or resid 276 through 300 or (resid 301 through 302 and (name N or \ name CA or name C or name O or name CB )) or resid 303 through 338)) } ncs_group { reference = (chain 'J' and (resid 2 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 78)) selection = (chain 'K' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 55 or (resid 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 through 78)) selection = (chain 'P' and resid 2 through 78) selection = (chain 'Q' and (resid 2 through 72 or (resid 73 and (name N or name CA or name C \ or name O or name CB )) or resid 74 through 75 or (resid 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 78)) selection = (chain 'R' and (resid 2 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 75 or (resid 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 78)) } 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: 0.920 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.490 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.005 0.083 27070 Z= 0.322 Angle : 0.845 11.145 37327 Z= 0.547 Chirality : 0.055 0.642 4237 Planarity : 0.006 0.081 4453 Dihedral : 18.848 179.486 10432 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.13 % Favored : 92.84 % Rotamer: Outliers : 0.68 % Allowed : 13.83 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.12), residues: 3086 helix: -2.58 (0.12), residues: 835 sheet: -0.13 (0.21), residues: 553 loop : -3.37 (0.11), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 265 TYR 0.020 0.002 TYR G 271 PHE 0.018 0.002 PHE G 95 TRP 0.018 0.002 TRP G 30 HIS 0.007 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.32 (27070) covalent geometry : angle 0.84482 / 0.55 (37327) hydrogen bonds : bond 0.15572 / 10.77 ( 927) hydrogen bonds : angle 5.99503 / 4.23 ( 2543) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 353 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: C 268 ARG cc_start: 0.5852 (ttt90) cc_final: 0.5146 (tpt90) REVERT: D 285 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: E 330 LEU cc_start: 0.8556 (pp) cc_final: 0.8026 (mt) REVERT: G 19 ASP cc_start: 0.6013 (t0) cc_final: 0.5774 (t0) REVERT: G 25 MET cc_start: 0.8350 (mtt) cc_final: 0.8076 (mtt) REVERT: L 117 MET cc_start: 0.6429 (mtm) cc_final: 0.6090 (mtm) REVERT: R 48 MET cc_start: 0.8829 (mmm) cc_final: 0.8545 (tpt) REVERT: R 66 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8317 (mttt) REVERT: B 203 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7462 (m-70) REVERT: B 222 ARG cc_start: 0.4115 (tpt170) cc_final: 0.3355 (ptp90) outliers start: 16 outliers final: 9 residues processed: 367 average time/residue: 0.2194 time to fit residues: 117.4636 Evaluate side-chains 265 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 254 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.0060 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 overall best weight: 3.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 ASN C 45 GLN C 69 GLN C 114 HIS C 168 GLN C 194 GLN C 196 HIS C 282 ASN C 293 HIS C 305 HIS D 77 GLN D 110 ASN D 223 GLN E 83 ASN E 223 GLN F 75 ASN F 77 GLN F 110 ASN G 32 GLN G 83 ASN G 164 HIS G 241 GLN H 32 GLN H 110 ASN H 262 ASN I 310 ASN J 65 ASN K 49 GLN P 58 ASN B 172 HIS B 255 ASN B 273 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131725 restraints weight = 35605.048| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.57 r_work: 0.3240 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 27070 Z= 0.234 Angle : 0.690 12.378 37327 Z= 0.377 Chirality : 0.047 0.391 4237 Planarity : 0.006 0.077 4453 Dihedral : 19.476 174.337 5126 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.10 % Favored : 92.87 % Rotamer: Outliers : 2.22 % Allowed : 16.18 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.13), residues: 3086 helix: -0.83 (0.16), residues: 833 sheet: 0.20 (0.22), residues: 543 loop : -3.09 (0.12), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 114 TYR 0.024 0.002 TYR H 285 PHE 0.018 0.002 PHE H 95 TRP 0.022 0.002 TRP G 30 HIS 0.008 0.001 HIS G 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (27070) covalent geometry : angle 0.69048 / 0.38 (37327) hydrogen bonds : bond 0.05791 / 3.92 ( 927) hydrogen bonds : angle 4.90267 / 3.47 ( 2543) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8146 (pp) REVERT: C 178 ARG cc_start: 0.7407 (mtt-85) cc_final: 0.6829 (ttp-170) REVERT: C 268 ARG cc_start: 0.6029 (ttt90) cc_final: 0.5191 (tpt90) REVERT: C 298 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7056 (mp) REVERT: F 76 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8768 (mt) REVERT: G 264 LEU cc_start: 0.7290 (mt) cc_final: 0.6963 (tp) REVERT: I 120 GLN cc_start: 0.8443 (mm110) cc_final: 0.8212 (mm110) REVERT: I 197 GLU cc_start: 0.8461 (tp30) cc_final: 0.8070 (tp30) REVERT: L 56 GLU cc_start: 0.7242 (mp0) cc_final: 0.6941 (mp0) REVERT: L 57 ARG cc_start: 0.8094 (mtp180) cc_final: 0.7836 (mtm180) REVERT: L 114 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6555 (mpp80) REVERT: L 117 MET cc_start: 0.5271 (mtm) cc_final: 0.4812 (mtm) REVERT: R 66 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8450 (mttt) REVERT: B 107 ASP cc_start: 0.9040 (t0) cc_final: 0.8831 (t0) REVERT: B 119 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8486 (mmmm) REVERT: B 153 ARG cc_start: 0.6721 (tpp-160) cc_final: 0.6512 (tpp-160) REVERT: B 203 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.8037 (m-70) REVERT: B 259 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.5947 (m-80) outliers start: 52 outliers final: 31 residues processed: 290 average time/residue: 0.2086 time to fit residues: 90.2461 Evaluate side-chains 279 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 299 optimal weight: 30.0000 chunk 216 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 260 optimal weight: 10.0000 chunk 43 optimal weight: 0.0370 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 193 optimal weight: 0.0170 chunk 121 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 GLN D 110 ASN D 324 HIS ** B 98 HIS ** 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 = 0.3804 r_free = 0.3804 target = 0.160739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130530 restraints weight = 36116.437| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.68 r_work: 0.3247 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 27070 Z= 0.117 Angle : 0.548 10.308 37327 Z= 0.305 Chirality : 0.042 0.392 4237 Planarity : 0.004 0.065 4453 Dihedral : 19.340 178.010 5118 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 2.05 % Allowed : 17.50 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3086 helix: -0.02 (0.17), residues: 840 sheet: 0.56 (0.23), residues: 541 loop : -2.82 (0.12), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 137 TYR 0.023 0.001 TYR G 271 PHE 0.010 0.001 PHE H 147 TRP 0.013 0.001 TRP I 174 HIS 0.004 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (27070) covalent geometry : angle 0.54807 / 0.31 (37327) hydrogen bonds : bond 0.04112 / 2.78 ( 927) hydrogen bonds : angle 4.40675 / 3.12 ( 2543) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 0.930 Fit side-chains REVERT: C 111 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7987 (pp) REVERT: C 180 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7172 (pp) REVERT: C 196 HIS cc_start: 0.8262 (t-90) cc_final: 0.7833 (t-170) REVERT: C 268 ARG cc_start: 0.5918 (ttt90) cc_final: 0.5448 (mtm-85) REVERT: C 298 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6694 (mp) REVERT: G 299 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7700 (mttt) REVERT: I 136 ARG cc_start: 0.8257 (mtm110) cc_final: 0.8057 (mtp-110) REVERT: L 56 GLU cc_start: 0.7312 (mp0) cc_final: 0.6921 (mp0) REVERT: L 57 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7744 (mtm180) REVERT: L 117 MET cc_start: 0.5287 (mtm) cc_final: 0.4812 (mtm) REVERT: B 220 GLU cc_start: 0.6528 (pp20) cc_final: 0.6121 (pp20) REVERT: B 222 ARG cc_start: 0.4368 (tpt170) cc_final: 0.3637 (ptp90) REVERT: B 259 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.5929 (m-80) outliers start: 48 outliers final: 25 residues processed: 305 average time/residue: 0.1982 time to fit residues: 91.3091 Evaluate side-chains 280 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 299 LYS Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 86 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 chunk 286 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 148 optimal weight: 0.3980 chunk 88 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN P 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.163046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132651 restraints weight = 35442.027| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.65 r_work: 0.3263 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27070 Z= 0.199 Angle : 0.628 11.834 37327 Z= 0.342 Chirality : 0.045 0.370 4237 Planarity : 0.005 0.070 4453 Dihedral : 19.291 177.644 5112 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.74 % Rotamer: Outliers : 2.48 % Allowed : 18.35 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.14), residues: 3086 helix: 0.19 (0.18), residues: 842 sheet: 0.44 (0.22), residues: 555 loop : -2.74 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 150 TYR 0.023 0.002 TYR G 271 PHE 0.018 0.002 PHE F 14 TRP 0.019 0.001 TRP G 30 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (27070) covalent geometry : angle 0.62848 / 0.34 (37327) hydrogen bonds : bond 0.05008 / 3.40 ( 927) hydrogen bonds : angle 4.50618 / 3.21 ( 2543) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 240 time to evaluate : 0.911 Fit side-chains REVERT: C 111 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8178 (pp) REVERT: C 180 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7313 (pp) REVERT: C 196 HIS cc_start: 0.8366 (t-90) cc_final: 0.7966 (t-170) REVERT: C 298 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6742 (mp) REVERT: D 285 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: F 76 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8753 (mt) REVERT: I 309 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8069 (m-30) REVERT: K 29 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8867 (mtp) REVERT: L 19 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: L 56 GLU cc_start: 0.7411 (mp0) cc_final: 0.6950 (mp0) REVERT: B 222 ARG cc_start: 0.4428 (tpt170) cc_final: 0.3658 (ptp90) REVERT: B 259 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6260 (m-80) outliers start: 58 outliers final: 39 residues processed: 280 average time/residue: 0.1883 time to fit residues: 79.9955 Evaluate side-chains 279 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 19 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain P residue 24 GLU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 2 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 312 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 278 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 313 optimal weight: 50.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 GLN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 HIS H 208 HIS R 15 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.158895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128227 restraints weight = 35270.392| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.66 r_work: 0.3213 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 27070 Z= 0.304 Angle : 0.767 13.922 37327 Z= 0.411 Chirality : 0.051 0.368 4237 Planarity : 0.006 0.072 4453 Dihedral : 19.435 176.051 5112 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.56 % Favored : 90.41 % Rotamer: Outliers : 3.33 % Allowed : 19.38 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.14), residues: 3086 helix: -0.09 (0.17), residues: 848 sheet: 0.25 (0.23), residues: 539 loop : -2.85 (0.13), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 150 TYR 0.024 0.003 TYR G 271 PHE 0.025 0.003 PHE F 14 TRP 0.028 0.002 TRP G 30 HIS 0.010 0.002 HIS G 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.30 (27070) covalent geometry : angle 0.76651 / 0.41 (37327) hydrogen bonds : bond 0.06320 / 4.31 ( 927) hydrogen bonds : angle 4.87900 / 3.48 ( 2543) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 247 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8272 (pp) REVERT: C 180 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7276 (pp) REVERT: F 76 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8827 (mt) REVERT: F 338 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: H 124 THR cc_start: 0.8403 (t) cc_final: 0.8119 (p) REVERT: H 136 ARG cc_start: 0.7843 (ptm160) cc_final: 0.7483 (ptm160) REVERT: H 288 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7316 (m) REVERT: I 309 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: K 29 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8830 (mtp) REVERT: L 56 GLU cc_start: 0.7428 (mp0) cc_final: 0.7155 (mp0) REVERT: B 153 ARG cc_start: 0.6750 (tpp-160) cc_final: 0.6495 (tpp-160) REVERT: B 203 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7959 (m-70) REVERT: B 222 ARG cc_start: 0.3906 (tpt170) cc_final: 0.3316 (ptp90) REVERT: B 255 ASN cc_start: 0.8501 (t0) cc_final: 0.8228 (t0) REVERT: B 259 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6088 (m-80) outliers start: 78 outliers final: 52 residues processed: 304 average time/residue: 0.1927 time to fit residues: 88.5785 Evaluate side-chains 302 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 241 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 307 LEU Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain J residue 29 MET Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain P residue 24 GLU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 179 optimal weight: 1.9990 chunk 116 optimal weight: 0.1980 chunk 255 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 156 optimal weight: 0.0570 chunk 215 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 271 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 324 HIS I 83 ASN J 65 ASN ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.165380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135480 restraints weight = 35350.648| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.60 r_work: 0.3321 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 27070 Z= 0.119 Angle : 0.563 10.901 37327 Z= 0.312 Chirality : 0.042 0.345 4237 Planarity : 0.004 0.075 4453 Dihedral : 19.183 179.024 5112 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 2.43 % Allowed : 20.49 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.15), residues: 3086 helix: 0.57 (0.18), residues: 841 sheet: 0.46 (0.23), residues: 544 loop : -2.56 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 175 TYR 0.017 0.001 TYR G 271 PHE 0.012 0.001 PHE H 147 TRP 0.016 0.001 TRP I 174 HIS 0.004 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (27070) covalent geometry : angle 0.56302 / 0.31 (37327) hydrogen bonds : bond 0.04067 / 2.80 ( 927) hydrogen bonds : angle 4.34235 / 3.08 ( 2543) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8075 (pp) REVERT: C 180 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7314 (pp) REVERT: C 240 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6362 (tt0) REVERT: C 298 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7277 (mp) REVERT: F 76 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8677 (mt) REVERT: F 338 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: H 136 ARG cc_start: 0.7896 (ptm160) cc_final: 0.7599 (ptm160) REVERT: L 56 GLU cc_start: 0.7483 (mp0) cc_final: 0.7204 (mp0) REVERT: B 203 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.8071 (m-70) REVERT: B 220 GLU cc_start: 0.6913 (pp20) cc_final: 0.6603 (pp20) REVERT: B 222 ARG cc_start: 0.4232 (tpt170) cc_final: 0.3758 (ptp90) REVERT: B 259 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6112 (m-80) outliers start: 57 outliers final: 31 residues processed: 284 average time/residue: 0.2051 time to fit residues: 88.6873 Evaluate side-chains 275 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 262 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 144 optimal weight: 0.3980 chunk 279 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN E 83 ASN ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.161756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131184 restraints weight = 35238.347| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.61 r_work: 0.3184 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27070 Z= 0.207 Angle : 0.638 12.039 37327 Z= 0.347 Chirality : 0.046 0.339 4237 Planarity : 0.005 0.071 4453 Dihedral : 19.213 179.156 5110 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.91 % Favored : 92.06 % Rotamer: Outliers : 2.52 % Allowed : 21.00 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.15), residues: 3086 helix: 0.44 (0.18), residues: 849 sheet: 0.41 (0.22), residues: 555 loop : -2.57 (0.13), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 175 TYR 0.019 0.002 TYR G 271 PHE 0.019 0.002 PHE F 14 TRP 0.019 0.002 TRP G 30 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (27070) covalent geometry : angle 0.63810 / 0.35 (37327) hydrogen bonds : bond 0.05007 / 3.42 ( 927) hydrogen bonds : angle 4.48093 / 3.18 ( 2543) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8153 (pp) REVERT: C 180 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7224 (pp) REVERT: C 240 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6378 (tt0) REVERT: C 272 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8496 (p0) REVERT: F 76 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8776 (mt) REVERT: F 148 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7837 (mt) REVERT: H 136 ARG cc_start: 0.7954 (ptm160) cc_final: 0.7628 (ptm160) REVERT: I 309 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: L 56 GLU cc_start: 0.7367 (mp0) cc_final: 0.7031 (mp0) REVERT: P 35 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8377 (mtt180) REVERT: B 203 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.8189 (m-70) REVERT: B 220 GLU cc_start: 0.6881 (pp20) cc_final: 0.6546 (pp20) REVERT: B 222 ARG cc_start: 0.4303 (tpt170) cc_final: 0.3907 (ptp90) REVERT: B 255 ASN cc_start: 0.8566 (t0) cc_final: 0.8265 (t0) REVERT: B 259 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6077 (m-80) outliers start: 59 outliers final: 39 residues processed: 282 average time/residue: 0.2117 time to fit residues: 90.0516 Evaluate side-chains 287 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain P residue 24 GLU Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 128 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130451 restraints weight = 35412.177| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.60 r_work: 0.3155 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 27070 Z= 0.248 Angle : 0.683 12.763 37327 Z= 0.369 Chirality : 0.047 0.343 4237 Planarity : 0.005 0.069 4453 Dihedral : 19.267 178.564 5110 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.72 % Favored : 91.25 % Rotamer: Outliers : 2.73 % Allowed : 20.96 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.14), residues: 3086 helix: 0.27 (0.18), residues: 849 sheet: 0.37 (0.22), residues: 550 loop : -2.63 (0.13), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 175 TYR 0.019 0.002 TYR I 285 PHE 0.020 0.002 PHE F 14 TRP 0.020 0.002 TRP G 30 HIS 0.008 0.001 HIS G 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (27070) covalent geometry : angle 0.68270 / 0.37 (37327) hydrogen bonds : bond 0.05441 / 3.72 ( 927) hydrogen bonds : angle 4.62113 / 3.28 ( 2543) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 242 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8182 (pp) REVERT: C 180 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7284 (pp) REVERT: C 240 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6341 (tt0) REVERT: C 272 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8545 (p0) REVERT: E 120 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7577 (tm-30) REVERT: F 76 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8812 (mt) REVERT: F 128 GLU cc_start: 0.8336 (pp20) cc_final: 0.7299 (pp20) REVERT: F 129 GLN cc_start: 0.7516 (mt0) cc_final: 0.6821 (mt0) REVERT: F 148 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7912 (mt) REVERT: F 338 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: H 136 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7620 (ptm160) REVERT: H 288 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.7323 (m) REVERT: I 309 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: L 56 GLU cc_start: 0.7388 (mp0) cc_final: 0.7039 (mp0) REVERT: P 35 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8376 (mtt180) REVERT: B 203 HIS cc_start: 0.8414 (OUTLIER) cc_final: 0.8189 (m-70) REVERT: B 222 ARG cc_start: 0.4088 (tpt170) cc_final: 0.3689 (ptp90) REVERT: B 255 ASN cc_start: 0.8535 (t0) cc_final: 0.8251 (t0) REVERT: B 259 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.5984 (m-80) outliers start: 64 outliers final: 44 residues processed: 289 average time/residue: 0.2061 time to fit residues: 90.0760 Evaluate side-chains 296 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 22 ASP Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 71 ILE Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 294 optimal weight: 0.2980 chunk 222 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.161889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134138 restraints weight = 35503.941| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.54 r_work: 0.3273 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27070 Z= 0.151 Angle : 0.595 12.005 37327 Z= 0.325 Chirality : 0.043 0.337 4237 Planarity : 0.004 0.068 4453 Dihedral : 19.180 179.568 5110 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.32 % Favored : 92.64 % Rotamer: Outliers : 2.52 % Allowed : 21.08 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.15), residues: 3086 helix: 0.55 (0.18), residues: 849 sheet: 0.55 (0.22), residues: 536 loop : -2.53 (0.13), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 175 TYR 0.017 0.002 TYR G 271 PHE 0.014 0.001 PHE H 147 TRP 0.017 0.001 TRP I 174 HIS 0.006 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (27070) covalent geometry : angle 0.59458 / 0.33 (37327) hydrogen bonds : bond 0.04501 / 3.08 ( 927) hydrogen bonds : angle 4.40472 / 3.12 ( 2543) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 234 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8085 (pp) REVERT: C 180 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7231 (pp) REVERT: C 240 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6290 (tt0) REVERT: C 272 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8503 (p0) REVERT: F 76 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8733 (mt) REVERT: F 148 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7835 (mt) REVERT: F 338 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: H 136 ARG cc_start: 0.7861 (ptm160) cc_final: 0.7535 (ptm160) REVERT: I 309 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: L 56 GLU cc_start: 0.7398 (mp0) cc_final: 0.7061 (mp0) REVERT: P 35 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8316 (mtt180) REVERT: B 203 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.8032 (m-70) REVERT: B 222 ARG cc_start: 0.4282 (tpt170) cc_final: 0.3689 (ptp90) REVERT: B 255 ASN cc_start: 0.8487 (t0) cc_final: 0.8174 (t0) REVERT: B 259 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6011 (m-80) outliers start: 59 outliers final: 42 residues processed: 280 average time/residue: 0.1885 time to fit residues: 80.0715 Evaluate side-chains 287 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 309 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain P residue 24 GLU Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 313 optimal weight: 50.0000 chunk 163 optimal weight: 0.6980 chunk 241 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 228 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 270 optimal weight: 0.9980 chunk 239 optimal weight: 7.9990 chunk 253 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 83 ASN ** B 98 HIS ** 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 = 0.3880 r_free = 0.3880 target = 0.166267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135940 restraints weight = 35255.633| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.66 r_work: 0.3255 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27070 Z= 0.111 Angle : 0.542 10.572 37327 Z= 0.298 Chirality : 0.041 0.325 4237 Planarity : 0.004 0.069 4453 Dihedral : 19.068 178.276 5110 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 1.96 % Allowed : 21.51 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.15), residues: 3086 helix: 0.84 (0.18), residues: 847 sheet: 0.63 (0.22), residues: 556 loop : -2.36 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 218 TYR 0.016 0.001 TYR G 271 PHE 0.012 0.001 PHE H 147 TRP 0.019 0.001 TRP I 174 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (27070) covalent geometry : angle 0.54159 / 0.30 (37327) hydrogen bonds : bond 0.03829 / 2.63 ( 927) hydrogen bonds : angle 4.16110 / 2.95 ( 2543) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6172 Ramachandran restraints generated. 3086 Oldfield, 0 Emsley, 3086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 244 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8013 (pp) REVERT: C 180 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7215 (pp) REVERT: C 272 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8386 (p0) REVERT: E 330 LEU cc_start: 0.7868 (pp) cc_final: 0.7548 (mt) REVERT: F 76 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8629 (mt) REVERT: H 136 ARG cc_start: 0.7891 (ptm160) cc_final: 0.7565 (ptm160) REVERT: L 56 GLU cc_start: 0.7432 (mp0) cc_final: 0.7084 (mp0) REVERT: P 35 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8370 (mtt180) REVERT: B 222 ARG cc_start: 0.4329 (tpt170) cc_final: 0.3729 (ptp90) REVERT: B 259 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6024 (m-80) outliers start: 46 outliers final: 36 residues processed: 279 average time/residue: 0.1933 time to fit residues: 81.9988 Evaluate side-chains 274 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 TRP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 25 PHE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 153 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 259 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 20.0000 chunk 211 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 155 optimal weight: 0.0470 chunk 122 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 151 ASN I 83 ASN ** B 98 HIS ** 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 = 0.3840 r_free = 0.3840 target = 0.162682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132131 restraints weight = 35266.558| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.60 r_work: 0.3278 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27070 Z= 0.189 Angle : 0.616 12.107 37327 Z= 0.334 Chirality : 0.045 0.324 4237 Planarity : 0.005 0.069 4453 Dihedral : 19.119 179.938 5110 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.78 % Favored : 92.19 % Rotamer: Outliers : 2.18 % Allowed : 21.47 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.15), residues: 3086 helix: 0.66 (0.18), residues: 851 sheet: 0.61 (0.22), residues: 548 loop : -2.41 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 175 TYR 0.016 0.002 TYR G 271 PHE 0.017 0.002 PHE F 14 TRP 0.018 0.001 TRP G 30 HIS 0.006 0.001 HIS G 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (27070) covalent geometry : angle 0.61593 / 0.33 (37327) hydrogen bonds : bond 0.04752 / 3.25 ( 927) hydrogen bonds : angle 4.35406 / 3.09 ( 2543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6329.49 seconds wall clock time: 108 minutes 47.09 seconds (6527.09 seconds total)