Starting phenix.real_space_refine on Sun Jul 5 06:26:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eqg_31265/07_2026/7eqg_31265_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eqg_31265/07_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_31265/07_2026/7eqg_31265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eqg_31265/07_2026/7eqg_31265.map" model { file = "/net/cci-nas-00/data/ceres_data/7eqg_31265/07_2026/7eqg_31265_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eqg_31265/07_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-dev-6108/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: 6.03, per 1000 atoms: 0.23 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: 2.10 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: 3.03 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: 5.11 Time building geometry restraints manager: 2.82 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: 36292 2.23 - 4.46: 917 4.46 - 6.69: 84 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=" O3' G M 48 " pdb=" C3' G M 48 " pdb=" C2' G M 48 " ideal model delta sigma weight residual 109.50 119.42 -9.92 1.50e+00 4.44e-01 4.38e+01 angle pdb=" C4' G M 48 " pdb=" C3' G M 48 " pdb=" O3' G M 48 " ideal model delta sigma weight residual 109.40 117.98 -8.58 1.50e+00 4.44e-01 3.27e+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=" N ARG B 258 " pdb=" CA ARG B 258 " pdb=" C ARG B 258 " ideal model delta sigma weight residual 108.90 100.59 8.31 1.63e+00 3.76e-01 2.60e+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: 4109 0.128 - 0.257: 125 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.700 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.090 ------------------------------------------------------------------------------- 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= 0.319 Angle : 0.835 11.145 37327 Z= 0.531 Chirality : 0.054 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 0.00529 / 0.32 (27070) covalent geometry : angle 0.83486 / 0.53 (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 : 0.933 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: 0.2227 time to fit residues: 118.4517 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 : 1.015 ------------------------------------------------------------------------------- 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: 20.0000 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 208 HIS G 241 GLN H 32 GLN H 110 ASN H 262 ASN I 310 ASN J 65 ASN 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 = 0.3832 r_free = 0.3832 target = 0.162123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131737 restraints weight = 35366.296| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.67 r_work: 0.3253 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27070 Z= 0.233 Angle : 0.681 12.234 37327 Z= 0.373 Chirality : 0.047 0.282 4237 Planarity : 0.006 0.076 4453 Dihedral : 19.517 174.924 5126 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.36 % Favored : 92.61 % Rotamer: Outliers : 2.26 % Allowed : 16.30 % Favored : 81.43 % 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: -2.65 (0.13), residues: 3086 helix: -0.81 (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 0.009 0.001 ARG B 14 TYR 0.022 0.002 TYR H 285 PHE 0.019 0.002 PHE F 14 TRP 0.021 0.002 TRP G 30 HIS 0.008 0.001 HIS C 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (27070) covalent geometry : angle 0.68130 / 0.37 (37327) hydrogen bonds : bond 0.05815 / 3.93 ( 927) hydrogen bonds : angle 4.90172 / 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 304 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8181 (pp) REVERT: C 178 ARG cc_start: 0.7352 (mtt-85) cc_final: 0.6829 (ttp-170) REVERT: C 268 ARG cc_start: 0.6016 (ttt90) cc_final: 0.5671 (mtm-85) REVERT: C 298 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6954 (mp) REVERT: F 76 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8753 (mt) REVERT: G 264 LEU cc_start: 0.7265 (mt) cc_final: 0.6976 (tp) REVERT: I 197 GLU cc_start: 0.8362 (tp30) cc_final: 0.7988 (tp30) REVERT: L 117 MET cc_start: 0.5462 (mtm) cc_final: 0.4988 (mtm) REVERT: R 66 LYS cc_start: 0.8761 (mtmm) cc_final: 0.8424 (mttt) REVERT: B 107 ASP cc_start: 0.8983 (t0) cc_final: 0.8776 (t0) REVERT: B 119 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8519 (mmmm) REVERT: B 203 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7912 (m-70) REVERT: B 259 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.5836 (m-80) outliers start: 53 outliers final: 31 residues processed: 292 average time/residue: 0.2013 time to fit residues: 87.9655 Evaluate side-chains 279 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 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: 20.0000 chunk 216 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 29 optimal weight: 0.0030 chunk 17 optimal weight: 10.0000 chunk 193 optimal weight: 0.0050 chunk 121 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.1408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 GLN D 110 ASN D 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.156141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125359 restraints weight = 36121.718| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.73 r_work: 0.3269 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27070 Z= 0.169 Angle : 0.604 12.103 37327 Z= 0.334 Chirality : 0.044 0.230 4237 Planarity : 0.005 0.062 4453 Dihedral : 19.423 175.426 5114 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.07 % Rotamer: Outliers : 2.35 % Allowed : 18.05 % Favored : 79.60 % 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: -2.18 (0.14), residues: 3086 helix: -0.18 (0.17), residues: 846 sheet: 0.39 (0.22), residues: 543 loop : -2.92 (0.12), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 150 TYR 0.023 0.002 TYR G 271 PHE 0.013 0.001 PHE H 95 TRP 0.016 0.001 TRP G 30 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (27070) covalent geometry : angle 0.60360 / 0.33 (37327) hydrogen bonds : bond 0.04853 / 3.29 ( 927) hydrogen bonds : angle 4.61013 / 3.28 ( 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 299 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.894 Fit side-chains REVERT: C 111 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8192 (pp) REVERT: C 178 ARG cc_start: 0.7378 (mtt-85) cc_final: 0.6905 (ttp-170) REVERT: C 180 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7349 (pp) REVERT: C 268 ARG cc_start: 0.6156 (ttt90) cc_final: 0.5594 (mtm-85) REVERT: C 298 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7141 (mp) REVERT: D 285 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: F 76 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8728 (mt) REVERT: I 120 GLN cc_start: 0.8521 (mm110) cc_final: 0.8271 (mm110) REVERT: B 107 ASP cc_start: 0.9107 (t0) cc_final: 0.8886 (t0) REVERT: B 203 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.8065 (m-70) REVERT: B 220 GLU cc_start: 0.6600 (pp20) cc_final: 0.6338 (pp20) REVERT: B 222 ARG cc_start: 0.4242 (tpt170) cc_final: 0.3729 (ptp90) REVERT: B 259 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6288 (m-80) outliers start: 55 outliers final: 32 residues processed: 283 average time/residue: 0.1840 time to fit residues: 79.1818 Evaluate side-chains 276 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 81 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 234 ASP Chi-restraints excluded: chain G residue 302 LEU 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 124 THR 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 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 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 259 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 86 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 286 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 173 GLN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN E 83 ASN I 83 ASN P 49 GLN R 15 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128700 restraints weight = 35518.909| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.67 r_work: 0.3223 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 27070 Z= 0.293 Angle : 0.730 14.044 37327 Z= 0.395 Chirality : 0.049 0.320 4237 Planarity : 0.006 0.067 4453 Dihedral : 19.460 175.209 5114 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.68 % Favored : 91.28 % Rotamer: Outliers : 3.07 % Allowed : 18.99 % Favored : 77.93 % 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: -2.21 (0.14), residues: 3086 helix: -0.18 (0.17), residues: 847 sheet: 0.24 (0.22), residues: 552 loop : -2.92 (0.13), residues: 1687 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 0.022 0.002 PHE F 14 TRP 0.026 0.002 TRP G 30 HIS 0.009 0.001 HIS G 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.29 (27070) covalent geometry : angle 0.72976 / 0.40 (37327) hydrogen bonds : bond 0.06064 / 4.12 ( 927) hydrogen bonds : angle 4.84326 / 3.45 ( 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 318 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 246 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8277 (pp) REVERT: C 180 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7245 (pp) REVERT: C 219 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5904 (pt) REVERT: F 76 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8815 (mt) REVERT: F 338 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: G 271 TYR cc_start: 0.8531 (p90) cc_final: 0.8227 (p90) REVERT: H 136 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7447 (ptm160) REVERT: I 309 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: L 19 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: B 203 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7910 (m-70) REVERT: B 222 ARG cc_start: 0.3911 (tpt170) cc_final: 0.3284 (ptp90) REVERT: B 255 ASN cc_start: 0.8466 (t0) cc_final: 0.8201 (t0) REVERT: B 259 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6188 (m-80) outliers start: 72 outliers final: 48 residues processed: 300 average time/residue: 0.1887 time to fit residues: 85.6256 Evaluate side-chains 295 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 C residue 219 ILE 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 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 119 LEU 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 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 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 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 153 GLN Chi-restraints excluded: chain P residue 24 GLU Chi-restraints excluded: chain Q residue 9 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 2 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 196 optimal weight: 0.4980 chunk 312 optimal weight: 0.0050 chunk 208 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 278 optimal weight: 0.9990 chunk 235 optimal weight: 0.3980 chunk 313 optimal weight: 50.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 324 HIS J 65 ASN ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.165259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.138125 restraints weight = 35324.566| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.52 r_work: 0.3322 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27070 Z= 0.114 Angle : 0.552 11.933 37327 Z= 0.306 Chirality : 0.042 0.223 4237 Planarity : 0.004 0.072 4453 Dihedral : 19.243 179.277 5114 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 2.13 % Allowed : 20.10 % Favored : 77.76 % 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: -1.64 (0.14), residues: 3086 helix: 0.46 (0.18), residues: 839 sheet: 0.54 (0.23), residues: 542 loop : -2.61 (0.13), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 175 TYR 0.018 0.001 TYR G 271 PHE 0.011 0.001 PHE H 147 TRP 0.015 0.001 TRP I 174 HIS 0.004 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (27070) covalent geometry : angle 0.55228 / 0.31 (37327) hydrogen bonds : bond 0.03937 / 2.69 ( 927) hydrogen bonds : angle 4.30863 / 3.06 ( 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 307 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7970 (pp) REVERT: C 178 ARG cc_start: 0.7378 (mtt-85) cc_final: 0.6880 (ttp-170) REVERT: C 180 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7196 (pp) REVERT: C 298 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7119 (mp) REVERT: F 338 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: G 271 TYR cc_start: 0.8300 (p90) cc_final: 0.7949 (p90) REVERT: H 136 ARG cc_start: 0.7798 (ptm160) cc_final: 0.7433 (ptm160) REVERT: I 309 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: L 19 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: L 30 GLN cc_start: 0.7031 (tp-100) cc_final: 0.6830 (tp40) REVERT: B 153 ARG cc_start: 0.6730 (tpp-160) cc_final: 0.6432 (tpp-160) REVERT: B 220 GLU cc_start: 0.6854 (pp20) cc_final: 0.6409 (pp20) REVERT: B 222 ARG cc_start: 0.3946 (tpt170) cc_final: 0.3529 (ptp90) REVERT: B 234 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 259 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6129 (m-80) outliers start: 50 outliers final: 30 residues processed: 291 average time/residue: 0.1997 time to fit residues: 88.3853 Evaluate side-chains 276 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 298 LEU Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain E 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 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 302 LEU Chi-restraints excluded: chain G residue 338 GLU 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 309 ASP Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 19 GLN Chi-restraints excluded: chain L residue 25 PHE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 179 optimal weight: 4.9990 chunk 116 optimal weight: 0.1980 chunk 255 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 271 optimal weight: 0.0070 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 49 GLN ** 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 = 0.3866 r_free = 0.3866 target = 0.165108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134671 restraints weight = 35427.288| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.61 r_work: 0.3245 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27070 Z= 0.129 Angle : 0.550 10.650 37327 Z= 0.305 Chirality : 0.042 0.208 4237 Planarity : 0.004 0.072 4453 Dihedral : 19.171 179.517 5112 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.51 % Favored : 93.45 % Rotamer: Outliers : 2.22 % Allowed : 20.79 % Favored : 77.00 % 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: -1.43 (0.15), residues: 3086 helix: 0.66 (0.18), residues: 842 sheet: 0.58 (0.22), residues: 550 loop : -2.49 (0.13), residues: 1694 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 0.011 0.001 PHE H 147 TRP 0.014 0.001 TRP I 174 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (27070) covalent geometry : angle 0.55049 / 0.30 (37327) hydrogen bonds : bond 0.04085 / 2.78 ( 927) hydrogen bonds : angle 4.23742 / 3.02 ( 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 290 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7996 (pp) REVERT: C 180 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7224 (pp) REVERT: C 240 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6307 (tt0) REVERT: F 76 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8656 (mt) REVERT: H 136 ARG cc_start: 0.7866 (ptm160) cc_final: 0.7511 (ptm160) REVERT: I 309 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: B 222 ARG cc_start: 0.4183 (tpt170) cc_final: 0.3566 (ptp90) REVERT: B 234 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6594 (mm-30) REVERT: B 259 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6038 (m-80) outliers start: 52 outliers final: 33 residues processed: 277 average time/residue: 0.1961 time to fit residues: 82.5510 Evaluate side-chains 269 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 D residue 151 ASN Chi-restraints excluded: chain E residue 76 LEU 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 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 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 134 THR Chi-restraints excluded: chain L residue 153 GLN 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 165 VAL 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: 10.0000 chunk 201 optimal weight: 0.2980 chunk 147 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 144 optimal weight: 0.0770 chunk 279 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 GLN E 83 ASN ** G 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3859 r_free = 0.3859 target = 0.164555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136916 restraints weight = 35335.469| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.51 r_work: 0.3309 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27070 Z= 0.128 Angle : 0.545 11.002 37327 Z= 0.301 Chirality : 0.042 0.226 4237 Planarity : 0.004 0.073 4453 Dihedral : 19.098 179.083 5110 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 2.35 % Allowed : 20.74 % Favored : 76.91 % 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: -1.27 (0.15), residues: 3086 helix: 0.82 (0.18), residues: 844 sheet: 0.69 (0.22), residues: 549 loop : -2.40 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 175 TYR 0.022 0.001 TYR G 271 PHE 0.012 0.001 PHE H 147 TRP 0.013 0.001 TRP I 174 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (27070) covalent geometry : angle 0.54539 / 0.30 (37327) hydrogen bonds : bond 0.04048 / 2.77 ( 927) hydrogen bonds : angle 4.16207 / 2.96 ( 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: 55 poor density : 245 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7964 (pp) REVERT: C 180 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7152 (pp) REVERT: C 219 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5847 (pt) REVERT: C 240 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: C 298 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6600 (mp) REVERT: F 76 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8642 (mt) REVERT: F 148 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7690 (mt) REVERT: F 338 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: H 136 ARG cc_start: 0.7823 (ptm160) cc_final: 0.7520 (ptm160) REVERT: P 35 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8327 (mtt180) REVERT: B 220 GLU cc_start: 0.6809 (pp20) cc_final: 0.6495 (pp20) REVERT: B 222 ARG cc_start: 0.4118 (tpt170) cc_final: 0.3723 (ptp90) REVERT: B 259 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.5980 (m-80) outliers start: 55 outliers final: 34 residues processed: 289 average time/residue: 0.1782 time to fit residues: 77.9373 Evaluate side-chains 277 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 219 ILE 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 288 VAL 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 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 78 THR 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 336 PHE 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 134 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 128 optimal weight: 7.9990 chunk 273 optimal weight: 7.9990 chunk 285 optimal weight: 0.4980 chunk 263 optimal weight: 9.9990 chunk 236 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 286 optimal weight: 0.0020 chunk 223 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 3.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 127 ASN E 83 ASN H 291 GLN ** B 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.161238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131162 restraints weight = 35388.065| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.59 r_work: 0.3164 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 27070 Z= 0.243 Angle : 0.665 13.189 37327 Z= 0.361 Chirality : 0.047 0.278 4237 Planarity : 0.005 0.069 4453 Dihedral : 19.197 178.565 5110 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.39 % Favored : 91.57 % Rotamer: Outliers : 2.52 % Allowed : 20.70 % Favored : 76.78 % 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: -1.56 (0.15), residues: 3086 helix: 0.49 (0.18), residues: 850 sheet: 0.57 (0.22), residues: 543 loop : -2.55 (0.13), residues: 1693 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 0.020 0.002 PHE F 14 TRP 0.022 0.002 TRP G 30 HIS 0.007 0.001 HIS G 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (27070) covalent geometry : angle 0.66492 / 0.36 (37327) hydrogen bonds : bond 0.05369 / 3.66 ( 927) hydrogen bonds : angle 4.50503 / 3.20 ( 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 296 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8154 (pp) REVERT: C 180 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7264 (pp) REVERT: C 240 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: C 272 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8543 (p0) REVERT: F 76 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8798 (mt) REVERT: F 148 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7857 (mt) REVERT: F 338 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: H 136 ARG cc_start: 0.7960 (ptm160) cc_final: 0.7624 (ptm160) REVERT: H 288 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7444 (m) REVERT: P 35 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8398 (mtt180) REVERT: B 203 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.8184 (m-70) REVERT: B 222 ARG cc_start: 0.4281 (tpt170) cc_final: 0.3896 (ptp90) REVERT: B 255 ASN cc_start: 0.8553 (t0) cc_final: 0.8268 (t0) REVERT: B 259 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.5996 (m-80) outliers start: 59 outliers final: 40 residues processed: 284 average time/residue: 0.1899 time to fit residues: 81.1869 Evaluate side-chains 287 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 272 ASP Chi-restraints excluded: chain C residue 322 VAL 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 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 270 TRP Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 49 VAL 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 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 249 VAL Chi-restraints excluded: chain I residue 336 PHE Chi-restraints excluded: chain J residue 53 GLU 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 134 THR 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 259 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 294 optimal weight: 0.0670 chunk 222 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 133 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.164500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134633 restraints weight = 35459.184| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.56 r_work: 0.3238 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27070 Z= 0.131 Angle : 0.560 11.776 37327 Z= 0.309 Chirality : 0.043 0.228 4237 Planarity : 0.004 0.071 4453 Dihedral : 19.119 179.224 5110 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.75 % Rotamer: Outliers : 2.05 % Allowed : 20.96 % Favored : 77.00 % 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: -1.32 (0.15), residues: 3086 helix: 0.81 (0.18), residues: 842 sheet: 0.59 (0.22), residues: 548 loop : -2.41 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 175 TYR 0.017 0.001 TYR G 271 PHE 0.013 0.001 PHE H 147 TRP 0.016 0.001 TRP I 174 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (27070) covalent geometry : angle 0.56019 / 0.31 (37327) hydrogen bonds : bond 0.04161 / 2.85 ( 927) hydrogen bonds : angle 4.25533 / 3.02 ( 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 283 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8074 (pp) REVERT: C 180 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7232 (pp) REVERT: C 240 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: C 272 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8424 (p0) REVERT: F 76 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8683 (mt) REVERT: F 148 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7809 (mt) REVERT: H 136 ARG cc_start: 0.7885 (ptm160) cc_final: 0.7607 (ptm160) REVERT: P 35 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8376 (mtt180) REVERT: B 222 ARG cc_start: 0.4298 (tpt170) cc_final: 0.3720 (ptp90) REVERT: B 259 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.5980 (m-80) outliers start: 48 outliers final: 32 residues processed: 272 average time/residue: 0.1812 time to fit residues: 74.8687 Evaluate side-chains 272 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 272 ASP Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain E residue 10 SER 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 148 LEU 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 283 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU 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 336 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 134 THR 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 313 optimal weight: 50.0000 chunk 163 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 181 optimal weight: 0.0000 chunk 228 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 270 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 253 optimal weight: 0.0770 overall best weight: 1.7746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3854 r_free = 0.3854 target = 0.163936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.136579 restraints weight = 35404.636| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.54 r_work: 0.3273 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27070 Z= 0.145 Angle : 0.567 11.982 37327 Z= 0.312 Chirality : 0.043 0.232 4237 Planarity : 0.004 0.069 4453 Dihedral : 19.082 179.344 5110 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.29 % Favored : 92.68 % Rotamer: Outliers : 1.88 % Allowed : 21.21 % Favored : 76.91 % 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: -1.27 (0.15), residues: 3086 helix: 0.82 (0.18), residues: 847 sheet: 0.64 (0.22), residues: 550 loop : -2.38 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 175 TYR 0.015 0.001 TYR G 271 PHE 0.012 0.001 PHE H 147 TRP 0.014 0.001 TRP G 30 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (27070) covalent geometry : angle 0.56674 / 0.31 (37327) hydrogen bonds : bond 0.04272 / 2.92 ( 927) hydrogen bonds : angle 4.22945 / 3.00 ( 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 280 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 111 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8052 (pp) REVERT: C 180 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7230 (pp) REVERT: C 240 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6252 (tt0) REVERT: C 272 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8398 (p0) REVERT: D 285 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: F 76 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8661 (mt) REVERT: F 148 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7811 (mt) REVERT: H 136 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7516 (ptm160) REVERT: P 35 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8377 (mtt180) REVERT: B 222 ARG cc_start: 0.4269 (tpt170) cc_final: 0.3714 (ptp90) REVERT: B 255 ASN cc_start: 0.8484 (t0) cc_final: 0.8164 (t0) REVERT: B 259 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.5907 (m-80) outliers start: 44 outliers final: 32 residues processed: 268 average time/residue: 0.2010 time to fit residues: 81.5070 Evaluate side-chains 274 residues out of total 2511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 272 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 10 SER 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 148 LEU 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 283 GLU Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 338 GLU 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 L residue 1 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 134 THR 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: 6.9990 chunk 210 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 146 optimal weight: 0.0170 chunk 309 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 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 = 0.3856 r_free = 0.3856 target = 0.164156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136698 restraints weight = 35400.559| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.49 r_work: 0.3284 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27070 Z= 0.144 Angle : 0.563 11.771 37327 Z= 0.310 Chirality : 0.043 0.226 4237 Planarity : 0.004 0.070 4453 Dihedral : 19.065 179.209 5110 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.61 % Favored : 93.36 % Rotamer: Outliers : 1.96 % Allowed : 21.21 % Favored : 76.82 % 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: 0.85 (0.18), residues: 845 sheet: 0.66 (0.22), residues: 550 loop : -2.36 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 175 TYR 0.016 0.001 TYR G 271 PHE 0.013 0.001 PHE H 147 TRP 0.013 0.001 TRP I 174 HIS 0.005 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (27070) covalent geometry : angle 0.56333 / 0.31 (37327) hydrogen bonds : bond 0.04225 / 2.89 ( 927) hydrogen bonds : angle 4.21270 / 2.99 ( 2543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6203.65 seconds wall clock time: 106 minutes 55.95 seconds (6415.95 seconds total)