Starting phenix.real_space_refine on Fri Aug 7 09:14:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k27_36830/08_2026/8k27_36830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k27_36830/08_2026/8k27_36830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k27_36830/08_2026/8k27_36830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k27_36830/08_2026/8k27_36830.map" model { file = "/net/cci-nas-00/data/ceres_data/8k27_36830/08_2026/8k27_36830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k27_36830/08_2026/8k27_36830.cif" } resolution = 3.6 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= 0.004 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 134 5.49 5 S 72 5.16 5 C 12914 2.51 5 N 3608 2.21 5 O 4455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21183 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1382 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1903 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1260 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 14, 'rna3p_pyr': 18} Link IDs: {'rna2p': 27, 'rna3p': 32} Chain: "Q" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1013 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "R" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2301 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2299 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1290 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Time building chain proxies: 3.31, per 1000 atoms: 0.16 Number of scatterers: 21183 At special positions: 0 Unit cell: (171.72, 131.76, 153.36, 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 72 16.00 P 134 15.00 O 4455 8.00 N 3608 7.00 C 12914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 590.8 milliseconds 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4372 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 43 sheets defined 27.1% alpha, 22.5% beta 37 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.798A pdb=" N ASP A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.544A pdb=" N ALA A 52 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.823A pdb=" N LYS A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.565A pdb=" N GLN A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.746A pdb=" N ILE A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.796A pdb=" N ASN A 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS A 152 " --> pdb=" O PRO A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 152' Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.732A pdb=" N MET A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.972A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 removed outlier: 3.575A pdb=" N PHE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.682A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.675A pdb=" N VAL B 223 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.623A pdb=" N ALA D 57 " --> pdb=" O PRO D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.521A pdb=" N THR D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.785A pdb=" N LEU D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 178 removed outlier: 3.726A pdb=" N ILE D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.579A pdb=" N ASN D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 233 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 287 through 298 Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.513A pdb=" N ALA C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.766A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 179 removed outlier: 3.973A pdb=" N ALA C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU C 168 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.825A pdb=" N ASN C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE C 233 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG C 234 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.509A pdb=" N LEU C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP C 275 " --> pdb=" O PHE C 271 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 298 removed outlier: 3.605A pdb=" N MET C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 58 removed outlier: 3.730A pdb=" N ALA G 57 " --> pdb=" O PRO G 54 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP G 58 " --> pdb=" O ASN G 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 54 through 58' Processing helix chain 'G' and resid 99 through 107 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.747A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN G 122 " --> pdb=" O ARG G 118 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 179 removed outlier: 3.643A pdb=" N MET G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 234 removed outlier: 3.629A pdb=" N ILE G 229 " --> pdb=" O HIS G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.500A pdb=" N LEU G 273 " --> pdb=" O ASP G 269 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP G 275 " --> pdb=" O PHE G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 298 Processing helix chain 'F' and resid 98 through 104 removed outlier: 3.527A pdb=" N GLN F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 126 removed outlier: 3.731A pdb=" N LEU F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 130 Processing helix chain 'F' and resid 164 through 178 removed outlier: 3.845A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 removed outlier: 3.704A pdb=" N ILE F 229 " --> pdb=" O HIS F 225 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA F 232 " --> pdb=" O LYS F 228 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG F 234 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 removed outlier: 3.739A pdb=" N ASN F 279 " --> pdb=" O ASP F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.773A pdb=" N GLN F 288 " --> pdb=" O THR F 284 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.708A pdb=" N ALA E 57 " --> pdb=" O PRO E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.871A pdb=" N THR E 105 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.752A pdb=" N LEU E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN E 122 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.767A pdb=" N ILE E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.579A pdb=" N ILE E 229 " --> pdb=" O HIS E 225 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG E 234 " --> pdb=" O GLY E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.938A pdb=" N ASP E 275 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN E 279 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 298 Processing helix chain 'H' and resid 54 through 58 removed outlier: 4.084A pdb=" N ALA H 57 " --> pdb=" O PRO H 54 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP H 58 " --> pdb=" O ASN H 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 58' Processing helix chain 'H' and resid 99 through 105 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.879A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 179 removed outlier: 3.658A pdb=" N MET H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 234 Processing helix chain 'H' and resid 269 through 280 Processing helix chain 'H' and resid 284 through 298 removed outlier: 3.664A pdb=" N PHE H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL H 291 " --> pdb=" O ASP H 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 61 through 69 removed outlier: 3.877A pdb=" N LEU I 65 " --> pdb=" O ASP I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 71 No H-bonds generated for 'chain 'I' and resid 70 through 71' Processing helix chain 'I' and resid 72 through 74 No H-bonds generated for 'chain 'I' and resid 72 through 74' Processing helix chain 'I' and resid 98 through 109 Processing helix chain 'I' and resid 112 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.770A pdb=" N GLY A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.770A pdb=" N GLY A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA B 205 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS B 191 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 207 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 185 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR B 213 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL B 183 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 215 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 142 removed outlier: 8.251A pdb=" N VAL B 24 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE A 166 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.093A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.093A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA B 94 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 6 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 138 " --> pdb=" O ILE B 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.734A pdb=" N TYR D 12 " --> pdb=" O GLY D 299 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 299 " --> pdb=" O TYR D 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 16 through 18 Processing sheet with id=AB2, first strand: chain 'D' and resid 16 through 18 Processing sheet with id=AB3, first strand: chain 'D' and resid 40 through 44 Processing sheet with id=AB4, first strand: chain 'D' and resid 217 through 218 Processing sheet with id=AB5, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.653A pdb=" N VAL D 260 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB7, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=AB8, first strand: chain 'C' and resid 16 through 18 removed outlier: 3.631A pdb=" N THR C 141 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 145 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 40 through 47 removed outlier: 3.528A pdb=" N PHE C 67 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 217 through 218 Processing sheet with id=AC2, first strand: chain 'C' and resid 254 through 255 Processing sheet with id=AC3, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.661A pdb=" N THR G 35 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.645A pdb=" N VAL G 145 " --> pdb=" O GLN G 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 40 through 45 Processing sheet with id=AC6, first strand: chain 'G' and resid 235 through 237 Processing sheet with id=AC7, first strand: chain 'G' and resid 254 through 255 Processing sheet with id=AC8, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AC9, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD1, first strand: chain 'F' and resid 40 through 45 removed outlier: 3.679A pdb=" N PHE F 67 " --> pdb=" O GLY F 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 217 through 218 Processing sheet with id=AD3, first strand: chain 'F' and resid 254 through 255 removed outlier: 3.784A pdb=" N VAL F 260 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 16 through 18 Processing sheet with id=AD5, first strand: chain 'E' and resid 16 through 18 Processing sheet with id=AD6, first strand: chain 'E' and resid 40 through 47 Processing sheet with id=AD7, first strand: chain 'E' and resid 217 through 218 Processing sheet with id=AD8, first strand: chain 'E' and resid 254 through 255 Processing sheet with id=AD9, first strand: chain 'H' and resid 92 through 94 removed outlier: 3.569A pdb=" N LEU H 94 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 16 through 18 Processing sheet with id=AE2, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.730A pdb=" N MET H 224 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 40 through 42 Processing sheet with id=AE4, first strand: chain 'H' and resid 235 through 237 Processing sheet with id=AE5, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AE6, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AE7, first strand: chain 'I' and resid 90 through 93 removed outlier: 3.711A pdb=" N GLU I 149 " --> pdb=" O ARG I 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE I 147 " --> pdb=" O VAL I 93 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4249 1.33 - 1.45: 5849 1.45 - 1.57: 11345 1.57 - 1.70: 264 1.70 - 1.82: 129 Bond restraints: 21836 Sorted by residual: bond pdb=" C LYS I 156 " pdb=" N PHE I 157 " ideal model delta sigma weight residual 1.331 1.509 -0.178 1.38e-02 5.25e+03 1.67e+02 bond pdb=" O3' A P 36 " pdb=" P G P 37 " ideal model delta sigma weight residual 1.607 1.462 0.145 1.20e-02 6.94e+03 1.46e+02 bond pdb=" O3' G P 37 " pdb=" P C P 38 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.20e-02 6.94e+03 2.54e+01 bond pdb=" O3' U P 35 " pdb=" P A P 36 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.20e-02 6.94e+03 2.26e+01 bond pdb=" O3' U P 9 " pdb=" P U P 10 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.20e-02 6.94e+03 2.23e+01 ... (remaining 21831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.33: 30196 14.33 - 28.66: 5 28.66 - 42.99: 1 42.99 - 57.32: 0 57.32 - 71.65: 1 Bond angle restraints: 30203 Sorted by residual: angle pdb=" O3' A P 36 " pdb=" P G P 37 " pdb=" O5' G P 37 " ideal model delta sigma weight residual 104.00 32.35 71.65 1.90e+00 2.77e-01 1.42e+03 angle pdb=" CA THR I 58 " pdb=" C THR I 58 " pdb=" N GLY I 59 " ideal model delta sigma weight residual 118.14 94.06 24.08 1.31e+00 5.83e-01 3.38e+02 angle pdb=" C3' A P 36 " pdb=" O3' A P 36 " pdb=" P G P 37 " ideal model delta sigma weight residual 119.70 99.14 20.56 1.20e+00 6.94e-01 2.93e+02 angle pdb=" O THR I 58 " pdb=" C THR I 58 " pdb=" N GLY I 59 " ideal model delta sigma weight residual 122.43 144.38 -21.95 1.34e+00 5.57e-01 2.68e+02 angle pdb=" C THR I 58 " pdb=" N GLY I 59 " pdb=" CA GLY I 59 " ideal model delta sigma weight residual 121.41 96.90 24.51 1.96e+00 2.60e-01 1.56e+02 ... (remaining 30198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 11835 35.45 - 70.89: 908 70.89 - 106.34: 53 106.34 - 141.79: 2 141.79 - 177.23: 10 Dihedral angle restraints: 12808 sinusoidal: 5965 harmonic: 6843 Sorted by residual: dihedral pdb=" O4' C P 44 " pdb=" C1' C P 44 " pdb=" N1 C P 44 " pdb=" C2 C P 44 " ideal model delta sinusoidal sigma weight residual 200.00 34.49 165.51 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" CB CYS A 152 " pdb=" SG CYS A 152 " pdb=" SG CYS A 156 " pdb=" CB CYS A 156 " ideal model delta sinusoidal sigma weight residual -86.00 -144.16 58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" C5' U P 35 " pdb=" C4' U P 35 " pdb=" C3' U P 35 " pdb=" O3' U P 35 " ideal model delta sinusoidal sigma weight residual 147.00 112.60 34.40 1 8.00e+00 1.56e-02 2.62e+01 ... (remaining 12805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3359 0.142 - 0.285: 125 0.285 - 0.427: 13 0.427 - 0.570: 3 0.570 - 0.712: 1 Chirality restraints: 3501 Sorted by residual: chirality pdb=" C3' C P 41 " pdb=" C4' C P 41 " pdb=" O3' C P 41 " pdb=" C2' C P 41 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA LYS I 124 " pdb=" N LYS I 124 " pdb=" C LYS I 124 " pdb=" CB LYS I 124 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CA PHE I 55 " pdb=" N PHE I 55 " pdb=" C PHE I 55 " pdb=" CB PHE I 55 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 3498 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 86 " -0.090 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO B 87 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 61 " 0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C ASP I 61 " -0.077 2.00e-02 2.50e+03 pdb=" O ASP I 61 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG I 62 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 58 " 0.013 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C THR I 58 " -0.061 2.00e-02 2.50e+03 pdb=" O THR I 58 " 0.027 2.00e-02 2.50e+03 pdb=" N GLY I 59 " 0.022 2.00e-02 2.50e+03 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 7 2.30 - 2.95: 9204 2.95 - 3.60: 28777 3.60 - 4.25: 49422 4.25 - 4.90: 80459 Nonbonded interactions: 167869 Sorted by model distance: nonbonded pdb=" CG1 VAL H 134 " pdb=" CZ PHE I 75 " model vdw 1.649 3.760 nonbonded pdb=" O3' A P 36 " pdb=" C5' G P 37 " model vdw 2.132 2.752 nonbonded pdb=" N THR I 58 " pdb=" N GLY I 59 " model vdw 2.158 2.560 nonbonded pdb=" O SER A 51 " pdb=" OG SER A 51 " model vdw 2.266 3.040 nonbonded pdb=" C3' A P 36 " pdb=" O5' G P 37 " model vdw 2.269 2.776 ... (remaining 167864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'D' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'F' and (resid 2 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'G' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'H' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 303)) } 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 group one per residue 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.400 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.006 0.178 21837 Z= 0.418 Angle : 1.164 71.649 30205 Z= 0.745 Chirality : 0.067 0.712 3501 Planarity : 0.006 0.134 3438 Dihedral : 21.737 177.233 8433 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.32 % Favored : 92.18 % Rotamer: Outliers : 11.13 % Allowed : 16.08 % Favored : 72.79 % Cbeta Deviations : 0.09 % 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: -3.25 (0.14), residues: 2378 helix: -2.58 (0.15), residues: 572 sheet: -0.12 (0.26), residues: 450 loop : -2.81 (0.13), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 133 TYR 0.057 0.002 TYR I 132 PHE 0.050 0.002 PHE E 182 TRP 0.049 0.002 TRP C 130 HIS 0.006 0.001 HIS I 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.42 (21836) covalent geometry : angle 1.16289 / 0.74 (30203) SS BOND : bond 0.00369 / 0.19 ( 1) SS BOND : angle 7.46609 / 4.00 ( 2) hydrogen bonds : bond 0.20377 / 13.20 ( 708) hydrogen bonds : angle 7.70195 / 5.40 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 293 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: A 142 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 195 ASN cc_start: 0.7882 (p0) cc_final: 0.7263 (t0) REVERT: D 58 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7736 (p0) REVERT: C 22 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8564 (mt) REVERT: C 30 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6643 (p0) REVERT: C 58 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8728 (p0) REVERT: F 58 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6336 (m-30) REVERT: F 59 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5966 (tptp) REVERT: H 86 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8623 (t) REVERT: H 127 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6303 (ttm110) REVERT: H 192 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6693 (tt) REVERT: H 211 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.5892 (mp) REVERT: H 213 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6497 (tppt) REVERT: H 228 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7059 (tttp) REVERT: H 260 VAL cc_start: 0.5983 (OUTLIER) cc_final: 0.5700 (m) REVERT: H 266 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6433 (p0) REVERT: H 281 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5857 (ttmm) outliers start: 218 outliers final: 28 residues processed: 430 average time/residue: 0.1270 time to fit residues: 83.8486 Evaluate side-chains 247 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.0570 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN B 84 ASN D 146 ASN D 231 ASN D 294 ASN G 294 ASN F 61 ASN F 203 GLN E 72 HIS H 132 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097290 restraints weight = 35416.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097957 restraints weight = 48592.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098554 restraints weight = 42419.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099072 restraints weight = 26815.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099557 restraints weight = 24346.540| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21837 Z= 0.154 Angle : 0.633 9.058 30205 Z= 0.358 Chirality : 0.045 0.351 3501 Planarity : 0.005 0.087 3438 Dihedral : 21.539 176.383 4388 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.17 % Favored : 94.62 % Rotamer: Outliers : 3.98 % Allowed : 19.04 % Favored : 76.98 % 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: -2.25 (0.15), residues: 2378 helix: -0.97 (0.20), residues: 574 sheet: 0.39 (0.27), residues: 424 loop : -2.48 (0.13), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 63 TYR 0.017 0.001 TYR I 90 PHE 0.017 0.001 PHE B 64 TRP 0.016 0.001 TRP G 239 HIS 0.003 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (21836) covalent geometry : angle 0.63276 / 0.36 (30203) SS BOND : bond 0.00551 / 0.29 ( 1) SS BOND : angle 3.75318 / 2.09 ( 2) hydrogen bonds : bond 0.05358 / 3.36 ( 708) hydrogen bonds : angle 5.07666 / 3.50 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 196 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7877 (tpp80) REVERT: A 130 TYR cc_start: 0.8247 (t80) cc_final: 0.8007 (t80) REVERT: B 237 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7536 (p) REVERT: C 30 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6897 (p0) REVERT: C 99 TYR cc_start: 0.8458 (t80) cc_final: 0.8181 (t80) REVERT: G 228 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8410 (mmtt) REVERT: G 294 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.9060 (t0) REVERT: H 42 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.7046 (mtpt) REVERT: H 211 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5764 (mp) REVERT: H 213 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6687 (tppt) REVERT: H 266 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6157 (t0) REVERT: H 281 LYS cc_start: 0.6434 (OUTLIER) cc_final: 0.6229 (mtpp) REVERT: H 283 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7382 (mp) REVERT: I 104 ARG cc_start: 0.4842 (OUTLIER) cc_final: 0.2636 (ttp-170) outliers start: 78 outliers final: 38 residues processed: 258 average time/residue: 0.1159 time to fit residues: 47.6711 Evaluate side-chains 223 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 235 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093073 restraints weight = 35668.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094101 restraints weight = 48705.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094517 restraints weight = 42758.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.094991 restraints weight = 26889.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095436 restraints weight = 24393.103| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21837 Z= 0.179 Angle : 0.605 9.745 30205 Z= 0.338 Chirality : 0.045 0.350 3501 Planarity : 0.004 0.072 3438 Dihedral : 21.245 175.122 4343 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 5.21 % Allowed : 18.22 % Favored : 76.57 % 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: -1.84 (0.16), residues: 2378 helix: -0.32 (0.21), residues: 577 sheet: 0.65 (0.28), residues: 408 loop : -2.34 (0.14), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 22 TYR 0.014 0.002 TYR C 81 PHE 0.018 0.001 PHE I 75 TRP 0.021 0.001 TRP G 239 HIS 0.005 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (21836) covalent geometry : angle 0.60468 / 0.34 (30203) SS BOND : bond 0.00401 / 0.21 ( 1) SS BOND : angle 3.43923 / 1.94 ( 2) hydrogen bonds : bond 0.04940 / 3.10 ( 708) hydrogen bonds : angle 4.75123 / 3.27 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 186 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.7927 (tpp80) REVERT: B 198 MET cc_start: 0.8538 (mmm) cc_final: 0.8252 (mmm) REVERT: B 237 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7623 (p) REVERT: D 128 THR cc_start: 0.9541 (OUTLIER) cc_final: 0.9325 (m) REVERT: C 30 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7344 (p0) REVERT: C 99 TYR cc_start: 0.8474 (t80) cc_final: 0.7961 (t80) REVERT: C 185 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8303 (pt) REVERT: G 191 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7253 (mtt) REVERT: G 228 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8472 (mmtt) REVERT: H 211 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.5955 (mp) REVERT: H 213 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6693 (tppt) REVERT: H 281 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6177 (ttmm) REVERT: H 283 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7364 (mp) REVERT: I 1 TYR cc_start: 0.4987 (OUTLIER) cc_final: 0.4572 (m-80) REVERT: I 50 ASP cc_start: 0.7513 (p0) cc_final: 0.7290 (p0) REVERT: I 57 LYS cc_start: 0.3909 (OUTLIER) cc_final: 0.3273 (mttt) REVERT: I 69 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6904 (mp) REVERT: I 104 ARG cc_start: 0.4818 (OUTLIER) cc_final: 0.2666 (ttp-170) outliers start: 102 outliers final: 56 residues processed: 270 average time/residue: 0.1175 time to fit residues: 51.0200 Evaluate side-chains 245 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 1 TYR Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 168 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 241 optimal weight: 50.0000 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 GLN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN ** H 294 ASN ** 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 = 0.3544 r_free = 0.3544 target = 0.124168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088335 restraints weight = 35657.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088696 restraints weight = 46849.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.088954 restraints weight = 47453.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.089914 restraints weight = 28287.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090188 restraints weight = 23769.513| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 21837 Z= 0.277 Angle : 0.675 10.720 30205 Z= 0.373 Chirality : 0.048 0.350 3501 Planarity : 0.005 0.070 3438 Dihedral : 21.176 177.179 4332 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.52 % Favored : 93.19 % Rotamer: Outliers : 5.46 % Allowed : 18.94 % Favored : 75.60 % 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: -1.83 (0.16), residues: 2378 helix: -0.24 (0.21), residues: 575 sheet: 0.20 (0.26), residues: 462 loop : -2.30 (0.14), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 22 TYR 0.017 0.002 TYR H 240 PHE 0.020 0.002 PHE D 85 TRP 0.019 0.002 TRP G 239 HIS 0.007 0.002 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.28 (21836) covalent geometry : angle 0.67485 / 0.37 (30203) SS BOND : bond 0.00399 / 0.21 ( 1) SS BOND : angle 3.37147 / 1.92 ( 2) hydrogen bonds : bond 0.05389 / 3.41 ( 708) hydrogen bonds : angle 4.71093 / 3.23 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 177 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8487 (t80) cc_final: 0.7953 (t80) REVERT: B 166 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8150 (p) REVERT: B 237 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7701 (p) REVERT: D 128 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9328 (m) REVERT: D 130 TRP cc_start: 0.6967 (OUTLIER) cc_final: 0.6431 (m-10) REVERT: C 22 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8622 (mt) REVERT: C 30 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7716 (p0) REVERT: G 191 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7652 (mtt) REVERT: G 210 LYS cc_start: 0.7529 (ptmt) cc_final: 0.7048 (tttm) REVERT: F 130 TRP cc_start: 0.7396 (OUTLIER) cc_final: 0.7042 (m-10) REVERT: H 211 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6060 (mp) REVERT: H 213 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6676 (tppt) REVERT: H 266 ASN cc_start: 0.7094 (p0) cc_final: 0.6084 (t0) REVERT: H 281 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6520 (ttmm) REVERT: H 283 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7481 (mp) REVERT: I 50 ASP cc_start: 0.7736 (p0) cc_final: 0.7487 (p0) REVERT: I 91 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6005 (ptt180) REVERT: I 104 ARG cc_start: 0.5073 (OUTLIER) cc_final: 0.3102 (tmm160) outliers start: 107 outliers final: 61 residues processed: 266 average time/residue: 0.1190 time to fit residues: 51.0317 Evaluate side-chains 241 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 166 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 23 MET Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 130 TRP Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 91 ARG Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 146 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 100 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 74 GLN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** 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 = 0.3588 r_free = 0.3588 target = 0.127434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093482 restraints weight = 35330.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093492 restraints weight = 57954.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094486 restraints weight = 50004.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094599 restraints weight = 32846.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095802 restraints weight = 29016.480| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21837 Z= 0.119 Angle : 0.565 8.592 30205 Z= 0.317 Chirality : 0.044 0.335 3501 Planarity : 0.004 0.062 3438 Dihedral : 20.975 176.424 4326 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.96 % Favored : 94.83 % Rotamer: Outliers : 3.83 % Allowed : 20.42 % Favored : 75.75 % 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: -1.52 (0.16), residues: 2378 helix: 0.10 (0.22), residues: 574 sheet: 0.41 (0.27), residues: 444 loop : -2.12 (0.14), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 133 TYR 0.018 0.001 TYR F 99 PHE 0.013 0.001 PHE B 64 TRP 0.010 0.001 TRP G 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (21836) covalent geometry : angle 0.56467 / 0.32 (30203) SS BOND : bond 0.00342 / 0.18 ( 1) SS BOND : angle 2.50780 / 1.43 ( 2) hydrogen bonds : bond 0.04091 / 2.55 ( 708) hydrogen bonds : angle 4.43843 / 3.03 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 187 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7946 (tpp80) REVERT: B 172 GLU cc_start: 0.7420 (mp0) cc_final: 0.7002 (mp0) REVERT: B 237 THR cc_start: 0.7938 (m) cc_final: 0.7608 (p) REVERT: D 128 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9287 (m) REVERT: D 130 TRP cc_start: 0.6845 (OUTLIER) cc_final: 0.6145 (m-10) REVERT: C 22 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8321 (mt) REVERT: C 185 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8380 (pt) REVERT: G 191 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7561 (mtt) REVERT: G 210 LYS cc_start: 0.7512 (ptmt) cc_final: 0.7065 (tttm) REVERT: H 192 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6896 (tt) REVERT: H 211 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6340 (mp) REVERT: H 213 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6733 (tppt) REVERT: H 281 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6385 (ttmm) REVERT: H 283 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7460 (mp) REVERT: I 1 TYR cc_start: 0.5668 (OUTLIER) cc_final: 0.5157 (m-80) REVERT: I 50 ASP cc_start: 0.7621 (p0) cc_final: 0.7378 (p0) REVERT: I 57 LYS cc_start: 0.4037 (OUTLIER) cc_final: 0.3427 (mttt) REVERT: I 104 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.2901 (tmm160) outliers start: 75 outliers final: 42 residues processed: 244 average time/residue: 0.1184 time to fit residues: 46.4827 Evaluate side-chains 231 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 1 TYR Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 178 optimal weight: 9.9990 chunk 244 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 245 optimal weight: 0.0060 overall best weight: 0.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN D 146 ASN ** H 294 ASN ** 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 = 0.3609 r_free = 0.3609 target = 0.129067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095067 restraints weight = 35471.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094480 restraints weight = 54396.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095513 restraints weight = 51783.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095844 restraints weight = 32242.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096486 restraints weight = 29046.339| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21837 Z= 0.111 Angle : 0.541 9.126 30205 Z= 0.302 Chirality : 0.043 0.333 3501 Planarity : 0.004 0.058 3438 Dihedral : 20.843 177.310 4320 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer: Outliers : 3.73 % Allowed : 20.67 % Favored : 75.60 % 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: -1.27 (0.17), residues: 2378 helix: 0.41 (0.22), residues: 575 sheet: 0.62 (0.27), residues: 449 loop : -2.03 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 63 TYR 0.018 0.001 TYR H 240 PHE 0.016 0.001 PHE A 9 TRP 0.017 0.001 TRP G 130 HIS 0.002 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (21836) covalent geometry : angle 0.54077 / 0.30 (30203) SS BOND : bond 0.00380 / 0.20 ( 1) SS BOND : angle 2.25139 / 1.28 ( 2) hydrogen bonds : bond 0.03702 / 2.30 ( 708) hydrogen bonds : angle 4.28776 / 2.93 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 198 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7971 (tpp80) REVERT: B 172 GLU cc_start: 0.7376 (mp0) cc_final: 0.6934 (mp0) REVERT: B 237 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7498 (p) REVERT: B 240 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7837 (pmtt) REVERT: C 22 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8199 (mt) REVERT: G 191 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7397 (mtt) REVERT: G 210 LYS cc_start: 0.7560 (ptmt) cc_final: 0.7106 (tttm) REVERT: G 289 MET cc_start: 0.8011 (ptp) cc_final: 0.7773 (ptp) REVERT: H 192 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6909 (tt) REVERT: H 211 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6388 (mp) REVERT: H 213 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6705 (tppt) REVERT: H 266 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.5901 (t0) REVERT: H 281 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6361 (ttmm) REVERT: H 283 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7464 (mp) REVERT: I 1 TYR cc_start: 0.5805 (OUTLIER) cc_final: 0.5355 (m-80) REVERT: I 50 ASP cc_start: 0.7689 (p0) cc_final: 0.7452 (p0) REVERT: I 57 LYS cc_start: 0.3969 (OUTLIER) cc_final: 0.3390 (mttt) REVERT: I 104 ARG cc_start: 0.4680 (OUTLIER) cc_final: 0.3022 (tmm160) REVERT: I 144 PHE cc_start: 0.7882 (p90) cc_final: 0.7627 (p90) outliers start: 73 outliers final: 41 residues processed: 256 average time/residue: 0.1093 time to fit residues: 45.2582 Evaluate side-chains 235 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 221 GLN Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 1 TYR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 45 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** 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 = 0.3560 r_free = 0.3560 target = 0.125343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.091720 restraints weight = 35455.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.091568 restraints weight = 57893.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092415 restraints weight = 52573.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092718 restraints weight = 35782.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.093469 restraints weight = 31306.759| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21837 Z= 0.222 Angle : 0.611 9.677 30205 Z= 0.336 Chirality : 0.046 0.330 3501 Planarity : 0.004 0.058 3438 Dihedral : 20.839 176.996 4320 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.90 % Rotamer: Outliers : 3.88 % Allowed : 20.42 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.16), residues: 2378 helix: 0.37 (0.22), residues: 575 sheet: 0.46 (0.27), residues: 444 loop : -2.07 (0.14), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 133 TYR 0.017 0.002 TYR H 240 PHE 0.028 0.002 PHE B 64 TRP 0.014 0.001 TRP G 239 HIS 0.007 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 (21836) covalent geometry : angle 0.61080 / 0.34 (30203) SS BOND : bond 0.00402 / 0.21 ( 1) SS BOND : angle 2.71384 / 1.55 ( 2) hydrogen bonds : bond 0.04553 / 2.87 ( 708) hydrogen bonds : angle 4.38793 / 2.99 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 174 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8533 (t80) cc_final: 0.7968 (t80) REVERT: B 83 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8825 (m110) REVERT: B 182 MET cc_start: 0.8446 (ttm) cc_final: 0.8211 (ttm) REVERT: B 198 MET cc_start: 0.8579 (mmm) cc_final: 0.8208 (mmm) REVERT: B 237 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7597 (p) REVERT: B 240 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7877 (pmtt) REVERT: D 128 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9365 (m) REVERT: D 130 TRP cc_start: 0.6798 (OUTLIER) cc_final: 0.6216 (m-10) REVERT: C 185 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8348 (pt) REVERT: G 191 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7607 (mtt) REVERT: G 210 LYS cc_start: 0.7651 (ptmt) cc_final: 0.7206 (tttm) REVERT: F 99 TYR cc_start: 0.9036 (t80) cc_final: 0.8782 (t80) REVERT: H 192 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7096 (tt) REVERT: H 211 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6391 (mp) REVERT: H 213 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6780 (tppt) REVERT: H 266 ASN cc_start: 0.6900 (OUTLIER) cc_final: 0.5972 (t0) REVERT: H 281 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6671 (ttmm) REVERT: I 1 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.5577 (m-80) REVERT: I 50 ASP cc_start: 0.7611 (p0) cc_final: 0.7388 (p0) REVERT: I 57 LYS cc_start: 0.4086 (OUTLIER) cc_final: 0.3488 (mttt) REVERT: I 104 ARG cc_start: 0.4543 (OUTLIER) cc_final: 0.3023 (tmm160) REVERT: I 144 PHE cc_start: 0.7828 (p90) cc_final: 0.7572 (p90) outliers start: 76 outliers final: 44 residues processed: 235 average time/residue: 0.1190 time to fit residues: 44.9256 Evaluate side-chains 222 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 221 GLN Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 1 TYR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 140 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 52 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 81 optimal weight: 50.0000 chunk 207 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 142 GLN D 146 ASN C 33 ASN ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092831 restraints weight = 35347.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093207 restraints weight = 54776.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093848 restraints weight = 50491.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094200 restraints weight = 34002.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094643 restraints weight = 30099.737| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21837 Z= 0.139 Angle : 0.560 9.314 30205 Z= 0.310 Chirality : 0.043 0.327 3501 Planarity : 0.003 0.057 3438 Dihedral : 20.798 177.371 4320 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.26 % Favored : 94.58 % Rotamer: Outliers : 3.57 % Allowed : 20.93 % Favored : 75.50 % 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: -1.25 (0.17), residues: 2378 helix: 0.48 (0.22), residues: 574 sheet: 0.55 (0.27), residues: 449 loop : -2.02 (0.15), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 74 TYR 0.016 0.001 TYR A 73 PHE 0.016 0.001 PHE B 64 TRP 0.017 0.001 TRP G 130 HIS 0.004 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (21836) covalent geometry : angle 0.55965 / 0.31 (30203) SS BOND : bond 0.00381 / 0.20 ( 1) SS BOND : angle 2.44747 / 1.40 ( 2) hydrogen bonds : bond 0.04010 / 2.52 ( 708) hydrogen bonds : angle 4.30895 / 2.93 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 178 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7892 (tpp80) REVERT: B 83 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8862 (m110) REVERT: B 156 MET cc_start: 0.6172 (tpt) cc_final: 0.5409 (ttt) REVERT: B 182 MET cc_start: 0.8455 (ttm) cc_final: 0.8229 (ttm) REVERT: B 237 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7599 (p) REVERT: B 240 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7889 (pmtt) REVERT: D 128 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9284 (m) REVERT: D 130 TRP cc_start: 0.6632 (OUTLIER) cc_final: 0.5930 (m-10) REVERT: C 22 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8364 (mt) REVERT: C 185 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8343 (pt) REVERT: G 191 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7497 (mtt) REVERT: G 210 LYS cc_start: 0.7619 (ptmt) cc_final: 0.7190 (tttm) REVERT: H 192 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7053 (tt) REVERT: H 213 LYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6763 (tppt) REVERT: I 1 TYR cc_start: 0.6084 (OUTLIER) cc_final: 0.5628 (m-80) REVERT: I 57 LYS cc_start: 0.4067 (OUTLIER) cc_final: 0.3495 (mttt) REVERT: I 104 ARG cc_start: 0.4446 (OUTLIER) cc_final: 0.2960 (tmm160) outliers start: 70 outliers final: 43 residues processed: 233 average time/residue: 0.1268 time to fit residues: 47.4532 Evaluate side-chains 227 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 221 GLN Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 1 TYR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 140 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 151 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 206 optimal weight: 0.1980 chunk 233 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN ** H 294 ASN ** 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 = 0.3558 r_free = 0.3558 target = 0.125169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.090574 restraints weight = 35267.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.090788 restraints weight = 52503.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091424 restraints weight = 51543.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091706 restraints weight = 32162.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092266 restraints weight = 28622.488| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21837 Z= 0.189 Angle : 0.596 9.924 30205 Z= 0.326 Chirality : 0.045 0.323 3501 Planarity : 0.004 0.056 3438 Dihedral : 20.778 177.060 4314 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.27 % Favored : 93.57 % Rotamer: Outliers : 3.42 % Allowed : 21.29 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.16), residues: 2378 helix: 0.45 (0.22), residues: 574 sheet: 0.45 (0.27), residues: 444 loop : -2.01 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 133 TYR 0.018 0.002 TYR H 240 PHE 0.019 0.001 PHE B 64 TRP 0.013 0.001 TRP G 130 HIS 0.004 0.001 HIS D 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (21836) covalent geometry : angle 0.59572 / 0.33 (30203) SS BOND : bond 0.00368 / 0.19 ( 1) SS BOND : angle 2.56889 / 1.46 ( 2) hydrogen bonds : bond 0.04365 / 2.77 ( 708) hydrogen bonds : angle 4.37640 / 2.98 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.7934 (tpp80) REVERT: A 130 TYR cc_start: 0.8562 (t80) cc_final: 0.7992 (t80) REVERT: B 83 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8889 (m110) REVERT: B 182 MET cc_start: 0.8441 (ttm) cc_final: 0.8214 (ttm) REVERT: B 237 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7630 (p) REVERT: B 240 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7860 (pmtt) REVERT: D 4 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8659 (pp) REVERT: D 128 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9341 (m) REVERT: D 130 TRP cc_start: 0.6778 (OUTLIER) cc_final: 0.5944 (m-10) REVERT: C 185 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8365 (pt) REVERT: G 191 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7651 (mtt) REVERT: G 210 LYS cc_start: 0.7732 (ptmt) cc_final: 0.7308 (tttm) REVERT: H 192 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7145 (tt) REVERT: H 213 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6793 (tppt) REVERT: I 1 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5786 (m-80) REVERT: I 57 LYS cc_start: 0.4112 (OUTLIER) cc_final: 0.3517 (mttt) REVERT: I 104 ARG cc_start: 0.4405 (OUTLIER) cc_final: 0.2861 (tmm160) outliers start: 67 outliers final: 45 residues processed: 224 average time/residue: 0.1192 time to fit residues: 43.2595 Evaluate side-chains 225 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 1 TYR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 0.0010 chunk 214 optimal weight: 9.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 146 ASN ** H 294 ASN ** 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 = 0.3570 r_free = 0.3570 target = 0.126093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.091215 restraints weight = 35337.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.091004 restraints weight = 49993.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091754 restraints weight = 48835.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092065 restraints weight = 31544.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.092954 restraints weight = 27832.807| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21837 Z= 0.140 Angle : 0.573 12.161 30205 Z= 0.313 Chirality : 0.044 0.321 3501 Planarity : 0.003 0.056 3438 Dihedral : 20.752 177.368 4314 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.17 % Favored : 94.66 % Rotamer: Outliers : 3.06 % Allowed : 21.80 % Favored : 75.14 % 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: -1.19 (0.17), residues: 2378 helix: 0.54 (0.22), residues: 574 sheet: 0.55 (0.27), residues: 444 loop : -1.96 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 133 TYR 0.030 0.001 TYR H 240 PHE 0.017 0.001 PHE B 64 TRP 0.016 0.001 TRP G 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (21836) covalent geometry : angle 0.57308 / 0.31 (30203) SS BOND : bond 0.00387 / 0.20 ( 1) SS BOND : angle 2.40550 / 1.37 ( 2) hydrogen bonds : bond 0.04020 / 2.53 ( 708) hydrogen bonds : angle 4.34121 / 2.95 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7950 (tpp80) REVERT: A 130 TYR cc_start: 0.8521 (t80) cc_final: 0.7945 (t80) REVERT: B 83 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8849 (m110) REVERT: B 156 MET cc_start: 0.6068 (tpt) cc_final: 0.5473 (ttt) REVERT: B 182 MET cc_start: 0.8428 (ttm) cc_final: 0.8178 (ttm) REVERT: B 237 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7620 (p) REVERT: B 240 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7845 (pmtt) REVERT: D 4 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8622 (pp) REVERT: D 128 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9311 (m) REVERT: D 130 TRP cc_start: 0.6581 (OUTLIER) cc_final: 0.5868 (m-10) REVERT: C 185 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8305 (pt) REVERT: G 191 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7518 (mtt) REVERT: G 210 LYS cc_start: 0.7715 (ptmt) cc_final: 0.7326 (tttm) REVERT: H 192 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7114 (tt) REVERT: H 213 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6818 (tppt) REVERT: I 1 TYR cc_start: 0.6089 (OUTLIER) cc_final: 0.5622 (m-80) REVERT: I 57 LYS cc_start: 0.4035 (OUTLIER) cc_final: 0.3473 (mttt) REVERT: I 104 ARG cc_start: 0.4619 (OUTLIER) cc_final: 0.3037 (tmm160) outliers start: 60 outliers final: 42 residues processed: 223 average time/residue: 0.1219 time to fit residues: 44.5983 Evaluate side-chains 227 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 1 TYR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 105 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 146 ASN ** H 294 ASN ** 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 = 0.3564 r_free = 0.3564 target = 0.125625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.090914 restraints weight = 35463.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.090552 restraints weight = 48927.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.091265 restraints weight = 49825.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.091686 restraints weight = 30673.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092196 restraints weight = 27584.363| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21837 Z= 0.166 Angle : 0.582 10.014 30205 Z= 0.318 Chirality : 0.044 0.320 3501 Planarity : 0.004 0.055 3438 Dihedral : 20.747 177.277 4314 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.97 % Favored : 93.86 % Rotamer: Outliers : 3.01 % Allowed : 22.21 % Favored : 74.78 % 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: -1.21 (0.17), residues: 2378 helix: 0.56 (0.22), residues: 574 sheet: 0.50 (0.27), residues: 444 loop : -1.97 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 133 TYR 0.052 0.002 TYR H 262 PHE 0.019 0.001 PHE I 144 TRP 0.018 0.001 TRP G 239 HIS 0.004 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (21836) covalent geometry : angle 0.58176 / 0.32 (30203) SS BOND : bond 0.00388 / 0.20 ( 1) SS BOND : angle 2.49310 / 1.42 ( 2) hydrogen bonds : bond 0.04139 / 2.60 ( 708) hydrogen bonds : angle 4.35276 / 2.96 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.36 seconds wall clock time: 45 minutes 27.07 seconds (2727.07 seconds total)