Starting phenix.real_space_refine on Thu Jul 2 08:59:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y26_33586/07_2026/7y26_33586.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y26_33586/07_2026/7y26_33586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2026/7y26_33586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2026/7y26_33586.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2026/7y26_33586.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2026/7y26_33586.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2026/7y26_33586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y26_33586/07_2026/7y26_33586.cif" } resolution = 3.3 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= 0.007 sd= 0.154 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5117 2.51 5 N 1355 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8014 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2420 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 7, 'ARG:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1687 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Classifications: {'peptide': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'DPN:plan-1': 1, 'DPN:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1633 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 212} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1881 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'PHE:plan': 5, 'ARG:plan': 7, 'ASP:plan': 3, 'GLU:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "F" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 327 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 1.85, per 1000 atoms: 0.23 Number of scatterers: 8014 At special positions: 0 Unit cell: (92.02, 128.14, 129.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1489 8.00 N 1355 7.00 C 5117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 2 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 193 " 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 Links applied TRANS " DTR C 4 " - " PHE C 3 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 409.4 milliseconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN C 1 " pdb=" CB DTR C 4 " Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.578A pdb=" N ILE A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.942A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.916A pdb=" N ASP B 91 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.690A pdb=" N GLY B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.291A pdb=" N ARG B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 4.210A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 202 " --> pdb=" O VAL B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.812A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.879A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.794A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'E' and resid 42 through 71 Processing helix chain 'E' and resid 77 through 93 removed outlier: 3.858A pdb=" N TYR E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET E 93 " --> pdb=" O ASP E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 112 through 146 removed outlier: 4.022A pdb=" N ARG E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 127 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 removed outlier: 3.872A pdb=" N LYS E 152 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 175 removed outlier: 3.636A pdb=" N THR E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA E 165 " --> pdb=" O MET E 161 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL E 166 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP E 167 " --> pdb=" O THR E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 203 through 238 removed outlier: 5.486A pdb=" N VAL E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Proline residue: E 220 - end of helix removed outlier: 3.893A pdb=" N CYS E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR E 228 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 282 Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 287 through 301 removed outlier: 3.665A pdb=" N LYS E 291 " --> pdb=" O THR E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.783A pdb=" N CYS E 306 " --> pdb=" O TYR E 302 " (cutoff:3.500A) Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 319 through 326 removed outlier: 3.693A pdb=" N VAL E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 removed outlier: 3.608A pdb=" N ASN F 24 " --> pdb=" O LYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 44 removed outlier: 3.614A pdb=" N HIS F 44 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 48 removed outlier: 3.827A pdb=" N ASP F 48 " --> pdb=" O ALA F 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.645A pdb=" N ARG A 49 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A 317 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.538A pdb=" N TYR A 59 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA A 73 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N MET A 61 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 71 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP A 63 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU A 69 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 74 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS A 91 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP A 83 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS A 89 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 3.633A pdb=" N THR A 102 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 115 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A 116 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL A 135 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 153 removed outlier: 7.053A pdb=" N SER A 160 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS A 149 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 158 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N PHE A 151 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN A 156 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 161 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 178 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.913A pdb=" N SER A 189 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 202 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 234 removed outlier: 7.029A pdb=" N GLY A 244 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 232 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA A 242 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE A 234 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA A 240 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A 262 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP A 254 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU A 260 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 278 removed outlier: 4.087A pdb=" N SER A 275 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 306 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 298 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG A 304 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.724A pdb=" N PHE B 70 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 212 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 143 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.650A pdb=" N ARG D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.163A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 98 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 135 removed outlier: 3.571A pdb=" N THR D 231 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR D 163 " --> pdb=" O MET D 218 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 178 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 182 " --> pdb=" O TYR D 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 182 through 185 removed outlier: 3.604A pdb=" N GLY E 182 " --> pdb=" O THR E 194 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2594 1.34 - 1.46: 2021 1.46 - 1.58: 3492 1.58 - 1.70: 0 1.70 - 1.81: 74 Bond restraints: 8181 Sorted by residual: bond pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.51e+00 bond pdb=" C VAL D 64 " pdb=" O VAL D 64 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.10e-01 bond pdb=" CA GLU A 130 " pdb=" CB GLU A 130 " ideal model delta sigma weight residual 1.532 1.545 -0.013 1.51e-02 4.39e+03 6.93e-01 bond pdb=" CZ2 DTR C 4 " pdb=" CH2 DTR C 4 " ideal model delta sigma weight residual 1.382 1.366 0.016 2.00e-02 2.50e+03 6.55e-01 bond pdb=" C ALA A 287 " pdb=" N GLY A 288 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.39e-02 5.18e+03 6.52e-01 ... (remaining 8176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 10763 1.27 - 2.53: 324 2.53 - 3.80: 63 3.80 - 5.07: 20 5.07 - 6.33: 5 Bond angle restraints: 11175 Sorted by residual: angle pdb=" CA GLU A 130 " pdb=" CB GLU A 130 " pdb=" CG GLU A 130 " ideal model delta sigma weight residual 114.10 120.43 -6.33 2.00e+00 2.50e-01 1.00e+01 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.57e+00 angle pdb=" C ILE E 174 " pdb=" CA ILE E 174 " pdb=" CB ILE E 174 " ideal model delta sigma weight residual 111.29 106.80 4.49 1.64e+00 3.72e-01 7.49e+00 angle pdb=" CA MET D 180 " pdb=" CB MET D 180 " pdb=" CG MET D 180 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.72e+00 angle pdb=" C GLY D 197 " pdb=" N THR D 198 " pdb=" CA THR D 198 " ideal model delta sigma weight residual 122.40 126.07 -3.67 1.45e+00 4.76e-01 6.41e+00 ... (remaining 11170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4373 17.98 - 35.96: 294 35.96 - 53.94: 55 53.94 - 71.92: 7 71.92 - 89.90: 2 Dihedral angle restraints: 4731 sinusoidal: 1513 harmonic: 3218 Sorted by residual: dihedral pdb=" CB CYS E 115 " pdb=" SG CYS E 115 " pdb=" SG CYS E 193 " pdb=" CB CYS E 193 " ideal model delta sinusoidal sigma weight residual -86.00 -175.90 89.90 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 -178.60 -88.40 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CA THR D 160 " pdb=" C THR D 160 " pdb=" N TYR D 161 " pdb=" CA TYR D 161 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 857 0.032 - 0.065: 306 0.065 - 0.097: 107 0.097 - 0.129: 50 0.129 - 0.161: 7 Chirality restraints: 1327 Sorted by residual: chirality pdb=" CB VAL E 106 " pdb=" CA VAL E 106 " pdb=" CG1 VAL E 106 " pdb=" CG2 VAL E 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA MET D 180 " pdb=" N MET D 180 " pdb=" C MET D 180 " pdb=" CB MET D 180 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ILE D 58 " pdb=" N ILE D 58 " pdb=" C ILE D 58 " pdb=" CB ILE D 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1324 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 48 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO F 49 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 49 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 49 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 214 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C ILE E 214 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE E 214 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU E 215 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 74 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO D 75 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.021 5.00e-02 4.00e+02 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 707 2.74 - 3.28: 7563 3.28 - 3.82: 12108 3.82 - 4.36: 12622 4.36 - 4.90: 24172 Nonbonded interactions: 57172 Sorted by model distance: nonbonded pdb=" O LEU D 153 " pdb=" OG1 THR D 160 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG D 67 " pdb=" OD2 ASP D 90 " model vdw 2.297 3.120 nonbonded pdb=" NZ LYS D 151 " pdb=" O SER D 152 " model vdw 2.299 3.120 nonbonded pdb=" O GLY A 224 " pdb=" NH1 ARG A 251 " model vdw 2.308 3.120 nonbonded pdb=" O TYR B 170 " pdb=" NH2 ARG B 188 " model vdw 2.326 3.120 ... (remaining 57167 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.003 0.031 8185 Z= 0.138 Angle : 0.566 6.332 11184 Z= 0.315 Chirality : 0.042 0.161 1327 Planarity : 0.004 0.043 1417 Dihedral : 12.652 70.709 2639 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 0.69 (0.25), residues: 1081 helix: 2.36 (0.27), residues: 372 sheet: 0.86 (0.32), residues: 254 loop : -1.50 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 241 TYR 0.020 0.002 TYR E 50 PHE 0.017 0.002 PHE A 278 TRP 0.018 0.001 TRP B 96 HIS 0.007 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8181) covalent geometry : angle 0.56569 / 0.31 (11175) SS BOND : bond 0.00387 / 0.19 ( 3) SS BOND : angle 1.19140 / 0.72 ( 6) hydrogen bonds : bond 0.12110 / 8.64 ( 402) hydrogen bonds : angle 4.66892 / 3.38 ( 1155) link_TRANS : bond 0.00085 / 0.04 ( 1) link_TRANS : angle 0.27719 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.222 Fit side-chains REVERT: A 188 MET cc_start: 0.8419 (mmm) cc_final: 0.8012 (mmm) REVERT: B 194 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7606 (ttm110) REVERT: D 159 ASN cc_start: 0.8397 (m-40) cc_final: 0.8138 (m110) REVERT: E 119 MET cc_start: 0.7646 (mmm) cc_final: 0.7433 (mmm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0783 time to fit residues: 15.9546 Evaluate side-chains 117 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN B 146 GLN B 239 ASN B 244 ASN E 308 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.169790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133010 restraints weight = 12982.777| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.45 r_work: 0.3572 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8185 Z= 0.140 Angle : 0.549 6.126 11184 Z= 0.298 Chirality : 0.043 0.152 1327 Planarity : 0.004 0.039 1417 Dihedral : 4.330 48.856 1178 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.92 % Allowed : 9.35 % Favored : 89.72 % 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: 0.77 (0.26), residues: 1081 helix: 2.36 (0.27), residues: 374 sheet: 0.76 (0.32), residues: 266 loop : -1.36 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.018 0.002 TYR A 105 PHE 0.018 0.002 PHE A 278 TRP 0.011 0.001 TRP E 108 HIS 0.007 0.002 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8181) covalent geometry : angle 0.54820 / 0.30 (11175) SS BOND : bond 0.00495 / 0.24 ( 3) SS BOND : angle 1.09192 / 0.66 ( 6) hydrogen bonds : bond 0.04898 / 3.54 ( 402) hydrogen bonds : angle 4.12007 / 2.92 ( 1155) link_TRANS : bond 0.00123 / 0.06 ( 1) link_TRANS : angle 0.70444 / 0.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.294 Fit side-chains REVERT: A 188 MET cc_start: 0.8530 (mmm) cc_final: 0.8018 (mmm) REVERT: B 126 LYS cc_start: 0.8149 (tttp) cc_final: 0.7818 (ttpp) REVERT: B 194 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7615 (ttm110) REVERT: D 159 ASN cc_start: 0.8597 (m-40) cc_final: 0.8147 (m110) REVERT: D 180 MET cc_start: 0.6686 (pmm) cc_final: 0.5923 (pmm) outliers start: 7 outliers final: 4 residues processed: 130 average time/residue: 0.0803 time to fit residues: 14.5879 Evaluate side-chains 112 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain D residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.129574 restraints weight = 12920.799| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.41 r_work: 0.3531 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8185 Z= 0.180 Angle : 0.586 6.477 11184 Z= 0.320 Chirality : 0.044 0.211 1327 Planarity : 0.004 0.042 1417 Dihedral : 4.533 48.163 1178 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.45 % Allowed : 12.91 % Favored : 85.64 % 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: 0.53 (0.26), residues: 1081 helix: 2.12 (0.27), residues: 375 sheet: 0.60 (0.32), residues: 270 loop : -1.45 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.024 0.002 TYR A 105 PHE 0.018 0.002 PHE A 241 TRP 0.015 0.002 TRP A 332 HIS 0.008 0.002 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 8181) covalent geometry : angle 0.58591 / 0.32 (11175) SS BOND : bond 0.00568 / 0.27 ( 3) SS BOND : angle 1.18597 / 0.71 ( 6) hydrogen bonds : bond 0.05608 / 4.06 ( 402) hydrogen bonds : angle 4.26063 / 3.03 ( 1155) link_TRANS : bond 0.00070 / 0.04 ( 1) link_TRANS : angle 0.84251 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.306 Fit side-chains REVERT: A 188 MET cc_start: 0.8512 (mmm) cc_final: 0.8011 (mmm) REVERT: B 126 LYS cc_start: 0.8201 (tttp) cc_final: 0.7875 (ttpp) REVERT: D 159 ASN cc_start: 0.8642 (m-40) cc_final: 0.8096 (m110) REVERT: D 180 MET cc_start: 0.6839 (pmm) cc_final: 0.6316 (pmm) outliers start: 11 outliers final: 5 residues processed: 126 average time/residue: 0.0730 time to fit residues: 13.3555 Evaluate side-chains 113 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 223 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 81 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 0.0050 chunk 52 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.172153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138423 restraints weight = 13092.102| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.57 r_work: 0.3554 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8185 Z= 0.101 Angle : 0.491 5.608 11184 Z= 0.267 Chirality : 0.041 0.162 1327 Planarity : 0.003 0.036 1417 Dihedral : 4.021 44.371 1178 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.45 % Allowed : 13.70 % Favored : 84.85 % 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: 0.77 (0.26), residues: 1081 helix: 2.32 (0.27), residues: 377 sheet: 0.66 (0.32), residues: 280 loop : -1.32 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 140 TYR 0.009 0.001 TYR A 124 PHE 0.015 0.001 PHE A 199 TRP 0.019 0.001 TRP A 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 8181) covalent geometry : angle 0.49070 / 0.27 (11175) SS BOND : bond 0.00399 / 0.19 ( 3) SS BOND : angle 0.73311 / 0.45 ( 6) hydrogen bonds : bond 0.03779 / 2.72 ( 402) hydrogen bonds : angle 3.85155 / 2.72 ( 1155) link_TRANS : bond 0.00095 / 0.05 ( 1) link_TRANS : angle 0.81150 / 0.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.8464 (mmm) cc_final: 0.8256 (mmm) REVERT: B 126 LYS cc_start: 0.8128 (tttp) cc_final: 0.7813 (ttpp) REVERT: B 239 ASN cc_start: 0.8646 (t160) cc_final: 0.8094 (m-40) REVERT: D 3 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6866 (mp10) REVERT: E 217 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: F 48 ASP cc_start: 0.8226 (t70) cc_final: 0.7923 (p0) outliers start: 11 outliers final: 5 residues processed: 128 average time/residue: 0.0719 time to fit residues: 13.4565 Evaluate side-chains 116 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 217 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 99 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 31 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.169137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135339 restraints weight = 13140.194| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.49 r_work: 0.3513 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8185 Z= 0.131 Angle : 0.522 5.562 11184 Z= 0.284 Chirality : 0.042 0.151 1327 Planarity : 0.003 0.036 1417 Dihedral : 4.127 45.879 1178 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.50 % Allowed : 14.23 % Favored : 83.27 % 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: 0.71 (0.26), residues: 1081 helix: 2.32 (0.27), residues: 372 sheet: 0.61 (0.32), residues: 279 loop : -1.35 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.019 0.002 TYR E 50 PHE 0.016 0.001 PHE A 199 TRP 0.021 0.001 TRP B 96 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8181) covalent geometry : angle 0.52121 / 0.28 (11175) SS BOND : bond 0.00440 / 0.21 ( 3) SS BOND : angle 0.89224 / 0.53 ( 6) hydrogen bonds : bond 0.04607 / 3.33 ( 402) hydrogen bonds : angle 3.96227 / 2.80 ( 1155) link_TRANS : bond 0.00094 / 0.05 ( 1) link_TRANS : angle 0.84001 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.362 Fit side-chains REVERT: A 188 MET cc_start: 0.8474 (mmm) cc_final: 0.7969 (mmm) REVERT: B 126 LYS cc_start: 0.8185 (tttp) cc_final: 0.7871 (ttpp) REVERT: B 197 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7323 (t80) REVERT: B 239 ASN cc_start: 0.8696 (t160) cc_final: 0.8248 (m-40) REVERT: D 159 ASN cc_start: 0.8694 (m-40) cc_final: 0.8127 (m110) REVERT: D 180 MET cc_start: 0.6712 (pmm) cc_final: 0.5727 (pmm) REVERT: E 217 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: F 48 ASP cc_start: 0.8296 (t70) cc_final: 0.7842 (p0) outliers start: 19 outliers final: 12 residues processed: 128 average time/residue: 0.0680 time to fit residues: 12.8418 Evaluate side-chains 125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain F residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN B 43 ASN ** E 125 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 = 0.4103 r_free = 0.4103 target = 0.169587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135654 restraints weight = 13084.046| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.54 r_work: 0.3526 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8185 Z= 0.120 Angle : 0.513 5.696 11184 Z= 0.279 Chirality : 0.042 0.151 1327 Planarity : 0.003 0.037 1417 Dihedral : 4.062 45.571 1178 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.11 % Allowed : 15.68 % Favored : 82.21 % 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: 0.68 (0.26), residues: 1081 helix: 2.30 (0.27), residues: 373 sheet: 0.49 (0.32), residues: 288 loop : -1.32 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.014 0.001 TYR A 105 PHE 0.016 0.001 PHE A 199 TRP 0.018 0.001 TRP B 96 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8181) covalent geometry : angle 0.51291 / 0.28 (11175) SS BOND : bond 0.00423 / 0.20 ( 3) SS BOND : angle 0.83180 / 0.49 ( 6) hydrogen bonds : bond 0.04333 / 3.13 ( 402) hydrogen bonds : angle 3.90857 / 2.76 ( 1155) link_TRANS : bond 0.00086 / 0.05 ( 1) link_TRANS : angle 0.83444 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.301 Fit side-chains REVERT: A 188 MET cc_start: 0.8487 (mmm) cc_final: 0.8260 (mmm) REVERT: B 126 LYS cc_start: 0.8153 (tttp) cc_final: 0.7842 (ttpp) REVERT: B 197 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7294 (t80) REVERT: B 239 ASN cc_start: 0.8682 (t160) cc_final: 0.8271 (m-40) REVERT: D 159 ASN cc_start: 0.8722 (m-40) cc_final: 0.8133 (m110) REVERT: D 180 MET cc_start: 0.6683 (pmm) cc_final: 0.5680 (pmm) REVERT: E 217 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: F 48 ASP cc_start: 0.8268 (t70) cc_final: 0.7847 (p0) outliers start: 16 outliers final: 11 residues processed: 126 average time/residue: 0.0642 time to fit residues: 11.8720 Evaluate side-chains 125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain F residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 83 optimal weight: 0.0060 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN E 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.173702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140812 restraints weight = 13076.992| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.23 r_work: 0.3582 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8185 Z= 0.092 Angle : 0.472 5.413 11184 Z= 0.254 Chirality : 0.040 0.146 1327 Planarity : 0.003 0.036 1417 Dihedral : 3.712 43.349 1178 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.45 % Allowed : 17.00 % Favored : 81.55 % 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: 0.88 (0.26), residues: 1081 helix: 2.49 (0.27), residues: 373 sheet: 0.75 (0.33), residues: 270 loop : -1.28 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 140 TYR 0.021 0.001 TYR E 50 PHE 0.014 0.001 PHE A 199 TRP 0.019 0.001 TRP B 96 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 ( 8181) covalent geometry : angle 0.47167 / 0.25 (11175) SS BOND : bond 0.00305 / 0.15 ( 3) SS BOND : angle 0.54770 / 0.32 ( 6) hydrogen bonds : bond 0.03236 / 2.33 ( 402) hydrogen bonds : angle 3.66646 / 2.57 ( 1155) link_TRANS : bond 0.00092 / 0.05 ( 1) link_TRANS : angle 0.78702 / 0.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.8461 (mmm) cc_final: 0.7986 (mmm) REVERT: B 126 LYS cc_start: 0.8095 (tttp) cc_final: 0.7841 (ttpp) REVERT: B 166 GLU cc_start: 0.7568 (tp30) cc_final: 0.7135 (tp30) REVERT: B 197 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7190 (t80) REVERT: B 239 ASN cc_start: 0.8631 (t160) cc_final: 0.8118 (m-40) REVERT: D 160 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7706 (t) REVERT: D 180 MET cc_start: 0.6546 (pmm) cc_final: 0.5896 (pmm) REVERT: E 161 MET cc_start: 0.7800 (tmm) cc_final: 0.7406 (tmm) REVERT: E 217 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: E 308 ASN cc_start: 0.8082 (t0) cc_final: 0.7802 (t0) REVERT: F 48 ASP cc_start: 0.8222 (t70) cc_final: 0.7855 (p0) outliers start: 11 outliers final: 7 residues processed: 134 average time/residue: 0.0604 time to fit residues: 11.8752 Evaluate side-chains 129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.168987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.137904 restraints weight = 13176.073| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.30 r_work: 0.3514 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8185 Z= 0.134 Angle : 0.538 8.743 11184 Z= 0.289 Chirality : 0.042 0.146 1327 Planarity : 0.003 0.038 1417 Dihedral : 3.981 46.008 1178 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.24 % Allowed : 17.00 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.26), residues: 1081 helix: 2.41 (0.27), residues: 372 sheet: 0.48 (0.32), residues: 290 loop : -1.24 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.019 0.002 TYR E 50 PHE 0.016 0.001 PHE A 199 TRP 0.023 0.001 TRP A 332 HIS 0.005 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 8181) covalent geometry : angle 0.53792 / 0.29 (11175) SS BOND : bond 0.00416 / 0.20 ( 3) SS BOND : angle 0.88379 / 0.51 ( 6) hydrogen bonds : bond 0.04468 / 3.24 ( 402) hydrogen bonds : angle 3.88168 / 2.74 ( 1155) link_TRANS : bond 0.00075 / 0.04 ( 1) link_TRANS : angle 0.84321 / 0.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.269 Fit side-chains REVERT: A 188 MET cc_start: 0.8466 (mmm) cc_final: 0.7935 (mmm) REVERT: B 126 LYS cc_start: 0.8123 (tttp) cc_final: 0.7871 (ttpp) REVERT: B 166 GLU cc_start: 0.7530 (tp30) cc_final: 0.7140 (tp30) REVERT: B 197 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7310 (t80) REVERT: B 239 ASN cc_start: 0.8671 (t160) cc_final: 0.8254 (m-40) REVERT: D 159 ASN cc_start: 0.8711 (m-40) cc_final: 0.8097 (m110) REVERT: D 180 MET cc_start: 0.6771 (pmm) cc_final: 0.5750 (pmm) REVERT: E 108 TRP cc_start: 0.8341 (t-100) cc_final: 0.7952 (t-100) REVERT: E 217 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: F 48 ASP cc_start: 0.8309 (t70) cc_final: 0.7894 (p0) outliers start: 17 outliers final: 10 residues processed: 127 average time/residue: 0.0676 time to fit residues: 12.4183 Evaluate side-chains 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain F residue 51 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 0.0020 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.172265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135360 restraints weight = 13051.916| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.45 r_work: 0.3600 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8185 Z= 0.097 Angle : 0.495 8.942 11184 Z= 0.264 Chirality : 0.041 0.146 1327 Planarity : 0.003 0.038 1417 Dihedral : 3.770 44.302 1178 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.84 % Allowed : 17.26 % Favored : 80.90 % 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: 0.87 (0.26), residues: 1081 helix: 2.50 (0.27), residues: 373 sheet: 0.55 (0.33), residues: 280 loop : -1.20 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 140 TYR 0.017 0.001 TYR E 50 PHE 0.015 0.001 PHE A 199 TRP 0.025 0.001 TRP B 96 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 8181) covalent geometry : angle 0.49439 / 0.26 (11175) SS BOND : bond 0.00338 / 0.16 ( 3) SS BOND : angle 0.61721 / 0.36 ( 6) hydrogen bonds : bond 0.03512 / 2.52 ( 402) hydrogen bonds : angle 3.69720 / 2.60 ( 1155) link_TRANS : bond 0.00098 / 0.05 ( 1) link_TRANS : angle 0.77189 / 0.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 188 MET cc_start: 0.8433 (mmm) cc_final: 0.8205 (mmm) REVERT: B 126 LYS cc_start: 0.8113 (tttp) cc_final: 0.7865 (ttpp) REVERT: B 166 GLU cc_start: 0.7572 (tp30) cc_final: 0.7150 (tp30) REVERT: B 197 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7218 (t80) REVERT: B 239 ASN cc_start: 0.8634 (t160) cc_final: 0.8111 (m-40) REVERT: D 46 GLU cc_start: 0.7668 (tp30) cc_final: 0.7107 (pt0) REVERT: D 180 MET cc_start: 0.6638 (pmm) cc_final: 0.5649 (pmm) REVERT: E 161 MET cc_start: 0.7853 (tmm) cc_final: 0.7444 (tmm) REVERT: E 217 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: F 48 ASP cc_start: 0.8262 (t70) cc_final: 0.7968 (p0) outliers start: 14 outliers final: 10 residues processed: 132 average time/residue: 0.0692 time to fit residues: 13.2758 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 91 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN E 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.168051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137007 restraints weight = 13153.941| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.30 r_work: 0.3503 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8185 Z= 0.144 Angle : 0.559 8.268 11184 Z= 0.300 Chirality : 0.043 0.140 1327 Planarity : 0.003 0.038 1417 Dihedral : 4.114 46.956 1178 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.24 % Allowed : 17.52 % Favored : 80.24 % 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: 0.73 (0.26), residues: 1081 helix: 2.38 (0.27), residues: 372 sheet: 0.58 (0.32), residues: 281 loop : -1.36 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.021 0.002 TYR E 50 PHE 0.016 0.001 PHE A 199 TRP 0.026 0.002 TRP E 108 HIS 0.006 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8181) covalent geometry : angle 0.55888 / 0.30 (11175) SS BOND : bond 0.00503 / 0.24 ( 3) SS BOND : angle 0.70531 / 0.42 ( 6) hydrogen bonds : bond 0.04717 / 3.41 ( 402) hydrogen bonds : angle 3.94276 / 2.80 ( 1155) link_TRANS : bond 0.00099 / 0.05 ( 1) link_TRANS : angle 0.82905 / 0.37 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.286 Fit side-chains REVERT: A 188 MET cc_start: 0.8428 (mmm) cc_final: 0.7893 (mmm) REVERT: B 126 LYS cc_start: 0.8137 (tttp) cc_final: 0.7827 (ttpp) REVERT: B 166 GLU cc_start: 0.7496 (tp30) cc_final: 0.7129 (tp30) REVERT: B 197 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7332 (t80) REVERT: B 239 ASN cc_start: 0.8678 (t160) cc_final: 0.8262 (m-40) REVERT: D 46 GLU cc_start: 0.7705 (tp30) cc_final: 0.7079 (pt0) REVERT: D 159 ASN cc_start: 0.8736 (m-40) cc_final: 0.8102 (m110) REVERT: D 180 MET cc_start: 0.6770 (pmm) cc_final: 0.5706 (pmm) REVERT: E 108 TRP cc_start: 0.8472 (t-100) cc_final: 0.8254 (t-100) REVERT: E 161 MET cc_start: 0.7864 (tmm) cc_final: 0.7445 (tmm) REVERT: E 217 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: F 48 ASP cc_start: 0.8431 (t70) cc_final: 0.8048 (p0) outliers start: 17 outliers final: 11 residues processed: 127 average time/residue: 0.0654 time to fit residues: 12.1735 Evaluate side-chains 127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 217 PHE Chi-restraints excluded: chain E residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN E 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.168537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135488 restraints weight = 13024.752| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.22 r_work: 0.3561 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8185 Z= 0.131 Angle : 0.546 8.296 11184 Z= 0.293 Chirality : 0.042 0.144 1327 Planarity : 0.003 0.038 1417 Dihedral : 4.114 46.607 1178 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.24 % Allowed : 17.52 % Favored : 80.24 % 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: 0.66 (0.26), residues: 1081 helix: 2.33 (0.27), residues: 373 sheet: 0.42 (0.32), residues: 288 loop : -1.35 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 140 TYR 0.020 0.002 TYR E 50 PHE 0.015 0.001 PHE A 199 TRP 0.025 0.001 TRP A 332 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8181) covalent geometry : angle 0.54569 / 0.29 (11175) SS BOND : bond 0.00443 / 0.21 ( 3) SS BOND : angle 0.78890 / 0.46 ( 6) hydrogen bonds : bond 0.04491 / 3.24 ( 402) hydrogen bonds : angle 3.90517 / 2.77 ( 1155) link_TRANS : bond 0.00076 / 0.04 ( 1) link_TRANS : angle 0.83263 / 0.37 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2127.97 seconds wall clock time: 36 minutes 59.64 seconds (2219.64 seconds total)