Starting phenix.real_space_refine on Wed Jan 14 15:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oz4_13120/01_2026/7oz4_13120.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oz4_13120/01_2026/7oz4_13120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oz4_13120/01_2026/7oz4_13120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oz4_13120/01_2026/7oz4_13120.map" model { file = "/net/cci-nas-00/data/ceres_data/7oz4_13120/01_2026/7oz4_13120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oz4_13120/01_2026/7oz4_13120.cif" } resolution = 3.9 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= 0.002 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 56 5.16 5 C 10391 2.51 5 N 3014 2.21 5 O 3245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16706 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2389 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 293} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2384 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 292} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2384 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 292} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2394 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2389 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 293} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2377 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 291} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2389 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 293} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 4.09, per 1000 atoms: 0.24 Number of scatterers: 16706 At special positions: 0 Unit cell: (157.3, 193.6, 133.1, 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 56 16.00 O 3245 8.00 N 3014 7.00 C 10391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 743.4 milliseconds 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3998 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 33 sheets defined 32.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.999A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 122 through 146 Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 202 through 214 removed outlier: 3.781A pdb=" N LEU A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 4.309A pdb=" N GLU A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'G' and resid 48 through 53 removed outlier: 4.036A pdb=" N SER G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 53' Processing helix chain 'G' and resid 111 through 117 removed outlier: 3.599A pdb=" N TRP G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 146 Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'G' and resid 176 through 178 No H-bonds generated for 'chain 'G' and resid 176 through 178' Processing helix chain 'G' and resid 202 through 213 removed outlier: 3.585A pdb=" N LEU G 206 " --> pdb=" O ASN G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 221 removed outlier: 3.725A pdb=" N ALA G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 216 through 221' Processing helix chain 'G' and resid 230 through 239 Processing helix chain 'G' and resid 247 through 259 Processing helix chain 'G' and resid 303 through 306 Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'F' and resid 111 through 117 removed outlier: 3.711A pdb=" N TRP F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 146 Processing helix chain 'F' and resid 167 through 175 Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 202 through 214 Processing helix chain 'F' and resid 216 through 221 removed outlier: 4.029A pdb=" N GLU F 221 " --> pdb=" O PRO F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 239 removed outlier: 3.526A pdb=" N LEU F 234 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 243 Processing helix chain 'F' and resid 247 through 260 Processing helix chain 'F' and resid 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.532A pdb=" N GLN B 82 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 83 " --> pdb=" O THR B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 122 through 146 Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 202 through 214 removed outlier: 3.791A pdb=" N LEU B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.975A pdb=" N GLU B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'E' and resid 48 through 53 removed outlier: 3.783A pdb=" N SER E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 53' Processing helix chain 'E' and resid 111 through 117 Processing helix chain 'E' and resid 122 through 146 removed outlier: 4.004A pdb=" N ILE E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 175 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 202 through 214 Processing helix chain 'E' and resid 216 through 221 removed outlier: 3.986A pdb=" N GLU E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 Proline residue: E 240 - end of helix removed outlier: 3.503A pdb=" N ARG E 244 " --> pdb=" O PRO E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 260 Processing helix chain 'E' and resid 323 through 325 No H-bonds generated for 'chain 'E' and resid 323 through 325' Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.149A pdb=" N GLN C 82 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN C 83 " --> pdb=" O THR C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'C' and resid 111 through 117 removed outlier: 3.869A pdb=" N TRP C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 146 Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.546A pdb=" N ARG C 244 " --> pdb=" O PRO C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.817A pdb=" N LEU D 50 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 122 through 146 Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 247 through 260 Processing helix chain 'D' and resid 304 through 306 No H-bonds generated for 'chain 'D' and resid 304 through 306' Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 4.119A pdb=" N GLN A 36 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.643A pdb=" N SER F 105 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.643A pdb=" N SER F 105 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 110 Processing sheet with id=AA7, first strand: chain 'A' and resid 180 through 181 removed outlier: 8.095A pdb=" N ILE A 269 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 227 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 271 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N CYS A 229 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.966A pdb=" N ILE A 191 " --> pdb=" O ALA A 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 54 through 57 removed outlier: 6.823A pdb=" N ASN G 54 " --> pdb=" O ILE G 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR G 291 " --> pdb=" O ASN G 54 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR G 56 " --> pdb=" O TYR G 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 54 through 57 removed outlier: 6.823A pdb=" N ASN G 54 " --> pdb=" O ILE G 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR G 291 " --> pdb=" O ASN G 54 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR G 56 " --> pdb=" O TYR G 291 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 62 through 63 Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 67 Processing sheet with id=AB4, first strand: chain 'G' and resid 180 through 181 removed outlier: 6.363A pdb=" N VAL G 227 " --> pdb=" O ILE G 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 54 through 56 Processing sheet with id=AB6, first strand: chain 'F' and resid 93 through 99 removed outlier: 3.690A pdb=" N GLY F 63 " --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN E 36 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU F 64 " --> pdb=" O GLN E 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 180 through 181 removed outlier: 8.335A pdb=" N ILE F 269 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL F 227 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AB9, first strand: chain 'B' and resid 54 through 58 Processing sheet with id=AC1, first strand: chain 'B' and resid 297 through 303 removed outlier: 3.829A pdb=" N SER B 314 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 76 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AC3, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AC4, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.613A pdb=" N ILE B 191 " --> pdb=" O ALA B 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 54 through 56 removed outlier: 6.392A pdb=" N ASN E 54 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR E 291 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR E 56 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 54 through 56 removed outlier: 6.392A pdb=" N ASN E 54 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR E 291 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR E 56 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 94 through 99 Processing sheet with id=AC8, first strand: chain 'E' and resid 180 through 181 removed outlier: 8.164A pdb=" N ILE E 269 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL E 227 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 191 through 192 removed outlier: 6.099A pdb=" N ILE E 191 " --> pdb=" O ALA E 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.365A pdb=" N LYS C 38 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU D 68 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU C 40 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N VAL D 70 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 54 through 58 removed outlier: 6.285A pdb=" N ASN C 54 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR C 291 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR C 56 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU C 293 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 58 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY C 295 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ASN C 316 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N GLY C 294 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N SER C 314 " --> pdb=" O GLY C 294 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N ARG C 296 " --> pdb=" O TYR C 312 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N TYR C 312 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N ARG C 298 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N GLU C 310 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N ILE C 300 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N ARG C 308 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 180 through 181 removed outlier: 3.955A pdb=" N GLU C 331 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLY C 278 " --> pdb=" O GLY C 230 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLY C 230 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 226 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N ILE C 269 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 227 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL C 271 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS C 229 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 54 through 58 removed outlier: 6.546A pdb=" N ASN D 54 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR D 291 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR D 56 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASN D 316 " --> pdb=" O GLN D 292 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 54 through 58 removed outlier: 6.546A pdb=" N ASN D 54 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TYR D 291 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TYR D 56 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASN D 316 " --> pdb=" O GLN D 292 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 180 through 181 682 hydrogen bonds defined for protein. 1908 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: 2.80 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3969 1.33 - 1.45: 3343 1.45 - 1.57: 9562 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 16965 Sorted by residual: bond pdb=" N PRO E 248 " pdb=" CD PRO E 248 " ideal model delta sigma weight residual 1.473 1.382 0.091 1.40e-02 5.10e+03 4.26e+01 bond pdb=" N PRO A 248 " pdb=" CD PRO A 248 " ideal model delta sigma weight residual 1.473 1.399 0.074 1.40e-02 5.10e+03 2.83e+01 bond pdb=" N PRO E 272 " pdb=" CD PRO E 272 " ideal model delta sigma weight residual 1.473 1.401 0.072 1.40e-02 5.10e+03 2.68e+01 bond pdb=" N PRO B 33 " pdb=" CD PRO B 33 " ideal model delta sigma weight residual 1.473 1.407 0.066 1.40e-02 5.10e+03 2.22e+01 bond pdb=" N PRO B 223 " pdb=" CD PRO B 223 " ideal model delta sigma weight residual 1.473 1.414 0.059 1.40e-02 5.10e+03 1.79e+01 ... (remaining 16960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 21369 1.37 - 2.74: 1447 2.74 - 4.11: 143 4.11 - 5.48: 17 5.48 - 6.86: 9 Bond angle restraints: 22985 Sorted by residual: angle pdb=" N PRO C 217 " pdb=" CA PRO C 217 " pdb=" CB PRO C 217 " ideal model delta sigma weight residual 103.48 110.01 -6.53 1.00e+00 1.00e+00 4.26e+01 angle pdb=" N PRO G 217 " pdb=" CA PRO G 217 " pdb=" CB PRO G 217 " ideal model delta sigma weight residual 103.48 109.93 -6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" N PRO F 217 " pdb=" CA PRO F 217 " pdb=" CB PRO F 217 " ideal model delta sigma weight residual 103.23 110.09 -6.86 1.07e+00 8.73e-01 4.11e+01 angle pdb=" N PRO B 217 " pdb=" CA PRO B 217 " pdb=" CB PRO B 217 " ideal model delta sigma weight residual 103.23 110.04 -6.81 1.07e+00 8.73e-01 4.05e+01 angle pdb=" N PRO E 217 " pdb=" CA PRO E 217 " pdb=" CB PRO E 217 " ideal model delta sigma weight residual 103.23 109.93 -6.70 1.07e+00 8.73e-01 3.92e+01 ... (remaining 22980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 9973 17.69 - 35.37: 299 35.37 - 53.06: 64 53.06 - 70.75: 27 70.75 - 88.43: 15 Dihedral angle restraints: 10378 sinusoidal: 4164 harmonic: 6214 Sorted by residual: dihedral pdb=" CA PRO F 33 " pdb=" C PRO F 33 " pdb=" N SER F 34 " pdb=" CA SER F 34 " ideal model delta harmonic sigma weight residual 180.00 -148.06 -31.94 0 5.00e+00 4.00e-02 4.08e+01 dihedral pdb=" CA THR A 103 " pdb=" C THR A 103 " pdb=" N ASN A 104 " pdb=" CA ASN A 104 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ARG A 297 " pdb=" C ARG A 297 " pdb=" N ARG A 298 " pdb=" CA ARG A 298 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 10375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1878 0.053 - 0.106: 464 0.106 - 0.160: 207 0.160 - 0.213: 16 0.213 - 0.266: 7 Chirality restraints: 2572 Sorted by residual: chirality pdb=" CA PRO G 217 " pdb=" N PRO G 217 " pdb=" C PRO G 217 " pdb=" CB PRO G 217 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA PRO C 217 " pdb=" N PRO C 217 " pdb=" C PRO C 217 " pdb=" CB PRO C 217 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA PRO D 217 " pdb=" N PRO D 217 " pdb=" C PRO D 217 " pdb=" CB PRO D 217 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2569 not shown) Planarity restraints: 3063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 129 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C ASP B 129 " 0.029 2.00e-02 2.50e+03 pdb=" O ASP B 129 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA B 130 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 128 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C ARG B 128 " -0.027 2.00e-02 2.50e+03 pdb=" O ARG B 128 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP B 129 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 141 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C MET B 141 " 0.026 2.00e-02 2.50e+03 pdb=" O MET B 141 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 142 " -0.009 2.00e-02 2.50e+03 ... (remaining 3060 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3047 2.77 - 3.30: 16880 3.30 - 3.83: 27048 3.83 - 4.37: 32766 4.37 - 4.90: 55303 Nonbonded interactions: 135044 Sorted by model distance: nonbonded pdb=" OG SER B 314 " pdb=" NH1 ARG C 85 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR E 87 " pdb=" ND1 HIS D 108 " model vdw 2.233 3.120 nonbonded pdb=" O ARG B 139 " pdb=" OH TYR B 319 " model vdw 2.248 3.040 nonbonded pdb=" O ASP E 106 " pdb=" OD1 ASP E 106 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" NH2 ARG B 126 " model vdw 2.346 3.120 ... (remaining 135039 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 'A' and resid 32 through 335) selection = (chain 'B' and resid 32 through 335) selection = chain 'C' selection = (chain 'D' and resid 32 through 335) selection = (chain 'E' and resid 32 through 335) selection = (chain 'F' and resid 32 through 335) selection = (chain 'G' and resid 32 through 335) } 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: 0.010 Normalize map: mean=0, sd=1: 26.040 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.700 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.010 0.091 16965 Z= 0.565 Angle : 0.732 6.856 22985 Z= 0.478 Chirality : 0.057 0.266 2572 Planarity : 0.003 0.034 3063 Dihedral : 10.766 88.433 6380 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.18), residues: 2125 helix: -0.19 (0.21), residues: 565 sheet: -1.93 (0.23), residues: 474 loop : -1.43 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 149 TYR 0.012 0.001 TYR C 291 PHE 0.013 0.001 PHE G 49 TRP 0.008 0.001 TRP B 117 HIS 0.004 0.001 HIS E 108 Details of bonding type rmsd covalent geometry : bond 0.01011 (16965) covalent geometry : angle 0.73161 (22985) hydrogen bonds : bond 0.16931 ( 660) hydrogen bonds : angle 8.22237 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 837 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8147 (mt0) cc_final: 0.7915 (mt0) REVERT: A 169 LEU cc_start: 0.8594 (mt) cc_final: 0.8193 (mt) REVERT: A 291 TYR cc_start: 0.8847 (p90) cc_final: 0.8497 (p90) REVERT: G 131 ILE cc_start: 0.8983 (mt) cc_final: 0.8762 (mt) REVERT: G 137 LEU cc_start: 0.8868 (tp) cc_final: 0.8424 (tt) REVERT: G 204 ASP cc_start: 0.8697 (m-30) cc_final: 0.8485 (m-30) REVERT: G 214 LEU cc_start: 0.8607 (mt) cc_final: 0.8288 (mt) REVERT: G 305 LYS cc_start: 0.8650 (tttt) cc_final: 0.8200 (mmpt) REVERT: G 319 TYR cc_start: 0.8507 (m-80) cc_final: 0.8161 (m-80) REVERT: F 84 ASP cc_start: 0.7518 (m-30) cc_final: 0.7311 (m-30) REVERT: F 85 ARG cc_start: 0.5651 (tpp80) cc_final: 0.4905 (mtp180) REVERT: F 97 ARG cc_start: 0.7374 (mmt90) cc_final: 0.7093 (mtt-85) REVERT: F 98 TYR cc_start: 0.8573 (p90) cc_final: 0.8174 (p90) REVERT: B 53 ILE cc_start: 0.8976 (mm) cc_final: 0.8741 (mm) REVERT: B 70 VAL cc_start: 0.8074 (m) cc_final: 0.7711 (m) REVERT: B 79 ASP cc_start: 0.7711 (t0) cc_final: 0.6857 (t0) REVERT: B 111 TYR cc_start: 0.8520 (m-10) cc_final: 0.8234 (m-80) REVERT: B 115 ASP cc_start: 0.8060 (m-30) cc_final: 0.7681 (t0) REVERT: B 135 GLN cc_start: 0.8662 (mt0) cc_final: 0.8035 (mt0) REVERT: B 163 ASP cc_start: 0.8333 (p0) cc_final: 0.8063 (p0) REVERT: B 209 ASP cc_start: 0.8007 (t70) cc_final: 0.6767 (t0) REVERT: B 281 VAL cc_start: 0.9553 (t) cc_final: 0.9313 (p) REVERT: B 286 ASN cc_start: 0.7905 (t0) cc_final: 0.7647 (t0) REVERT: E 98 TYR cc_start: 0.8689 (p90) cc_final: 0.8278 (p90) REVERT: E 122 ASP cc_start: 0.6352 (p0) cc_final: 0.5883 (p0) REVERT: E 126 ARG cc_start: 0.7844 (mtt-85) cc_final: 0.7490 (mmm160) REVERT: E 172 LEU cc_start: 0.8649 (tp) cc_final: 0.8420 (tp) REVERT: E 261 LYS cc_start: 0.8465 (mmtt) cc_final: 0.7909 (mmmt) REVERT: E 289 ILE cc_start: 0.8847 (mt) cc_final: 0.8611 (mt) REVERT: C 53 ILE cc_start: 0.8990 (mm) cc_final: 0.8627 (mm) REVERT: C 54 ASN cc_start: 0.8328 (m-40) cc_final: 0.8105 (m110) REVERT: C 64 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6225 (mt-10) REVERT: C 250 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8145 (tp40) REVERT: C 305 LYS cc_start: 0.8436 (mttt) cc_final: 0.7953 (tptt) REVERT: D 35 VAL cc_start: 0.8706 (t) cc_final: 0.8503 (m) REVERT: D 47 SER cc_start: 0.8478 (m) cc_final: 0.8058 (p) REVERT: D 209 ASP cc_start: 0.7488 (m-30) cc_final: 0.7126 (m-30) REVERT: D 227 VAL cc_start: 0.9004 (t) cc_final: 0.8783 (p) REVERT: D 247 ASP cc_start: 0.8058 (m-30) cc_final: 0.7714 (m-30) outliers start: 0 outliers final: 0 residues processed: 837 average time/residue: 0.1833 time to fit residues: 210.4806 Evaluate side-chains 433 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 61 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN A 158 ASN G 36 GLN G 112 GLN B 83 GLN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN B 311 ASN E 61 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN D 158 ASN D 165 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.116762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108008 restraints weight = 37311.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110310 restraints weight = 20126.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111888 restraints weight = 12359.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112914 restraints weight = 8283.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113694 restraints weight = 5991.633| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16965 Z= 0.164 Angle : 0.629 8.622 22985 Z= 0.334 Chirality : 0.047 0.216 2572 Planarity : 0.004 0.062 3063 Dihedral : 4.861 31.131 2377 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.40 % Allowed : 11.51 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 2125 helix: 0.54 (0.22), residues: 557 sheet: -1.76 (0.24), residues: 440 loop : -1.13 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 149 TYR 0.030 0.002 TYR B 312 PHE 0.023 0.002 PHE A 49 TRP 0.020 0.002 TRP E 218 HIS 0.004 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00366 (16965) covalent geometry : angle 0.62947 (22985) hydrogen bonds : bond 0.04813 ( 660) hydrogen bonds : angle 6.41830 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 478 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8183 (tt0) cc_final: 0.7855 (tt0) REVERT: A 86 GLU cc_start: 0.7741 (pm20) cc_final: 0.7439 (pm20) REVERT: A 135 GLN cc_start: 0.8394 (mt0) cc_final: 0.8027 (mt0) REVERT: A 142 ILE cc_start: 0.9233 (mt) cc_final: 0.9012 (mm) REVERT: A 203 LEU cc_start: 0.9196 (tp) cc_final: 0.8867 (tt) REVERT: A 291 TYR cc_start: 0.8743 (p90) cc_final: 0.8388 (p90) REVERT: G 65 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8728 (mtpp) REVERT: G 89 ASP cc_start: 0.7877 (t0) cc_final: 0.6680 (m-30) REVERT: G 133 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8361 (tppt) REVERT: G 160 MET cc_start: 0.8037 (pmm) cc_final: 0.7707 (mtt) REVERT: G 305 LYS cc_start: 0.8579 (tttt) cc_final: 0.8224 (mmpt) REVERT: G 319 TYR cc_start: 0.8754 (m-80) cc_final: 0.7811 (m-80) REVERT: F 85 ARG cc_start: 0.5623 (tpp80) cc_final: 0.3452 (mtm180) REVERT: B 53 ILE cc_start: 0.8883 (mm) cc_final: 0.8656 (mm) REVERT: B 56 TYR cc_start: 0.7209 (m-80) cc_final: 0.6885 (m-10) REVERT: B 70 VAL cc_start: 0.8433 (m) cc_final: 0.8094 (m) REVERT: B 93 MET cc_start: 0.8615 (mmt) cc_final: 0.8059 (mmt) REVERT: B 233 LEU cc_start: 0.8352 (mm) cc_final: 0.7701 (mm) REVERT: B 290 TYR cc_start: 0.7831 (m-80) cc_final: 0.7522 (m-80) REVERT: B 329 MET cc_start: 0.8169 (ptm) cc_final: 0.7826 (ptm) REVERT: E 98 TYR cc_start: 0.8668 (p90) cc_final: 0.8389 (p90) REVERT: E 104 ASN cc_start: 0.6708 (t0) cc_final: 0.5759 (m-40) REVERT: E 236 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8477 (t0) REVERT: E 261 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8350 (mmmt) REVERT: E 313 GLU cc_start: 0.6437 (mm-30) cc_final: 0.5405 (mm-30) REVERT: C 45 GLU cc_start: 0.7872 (mp0) cc_final: 0.7668 (mp0) REVERT: C 53 ILE cc_start: 0.8984 (mm) cc_final: 0.8769 (mm) REVERT: C 93 MET cc_start: 0.7305 (pmm) cc_final: 0.7040 (pmm) REVERT: C 152 THR cc_start: 0.8794 (m) cc_final: 0.8298 (p) REVERT: C 283 ARG cc_start: 0.7587 (ptm-80) cc_final: 0.7262 (ptm160) REVERT: C 285 ASP cc_start: 0.8756 (m-30) cc_final: 0.8244 (p0) REVERT: C 310 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7440 (mt-10) REVERT: D 35 VAL cc_start: 0.8960 (t) cc_final: 0.8550 (m) REVERT: D 47 SER cc_start: 0.8181 (m) cc_final: 0.7904 (p) REVERT: D 175 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: D 224 ASP cc_start: 0.8047 (m-30) cc_final: 0.7550 (t0) REVERT: D 227 VAL cc_start: 0.8968 (t) cc_final: 0.8657 (p) REVERT: D 329 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7656 (ptm) outliers start: 60 outliers final: 35 residues processed: 513 average time/residue: 0.1603 time to fit residues: 116.8957 Evaluate side-chains 428 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 390 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 329 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 85 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN B 213 HIS B 251 GLN E 37 GLN E 82 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103758 restraints weight = 38265.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106187 restraints weight = 20499.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107810 restraints weight = 12586.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108879 restraints weight = 8497.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109683 restraints weight = 6176.523| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16965 Z= 0.199 Angle : 0.627 6.656 22985 Z= 0.334 Chirality : 0.047 0.323 2572 Planarity : 0.005 0.061 3063 Dihedral : 4.838 31.734 2377 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.03 % Allowed : 14.01 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 2125 helix: 0.72 (0.22), residues: 551 sheet: -1.82 (0.23), residues: 430 loop : -1.16 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 231 TYR 0.020 0.002 TYR D 219 PHE 0.016 0.002 PHE E 49 TRP 0.010 0.002 TRP C 117 HIS 0.005 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00449 (16965) covalent geometry : angle 0.62715 (22985) hydrogen bonds : bond 0.04650 ( 660) hydrogen bonds : angle 6.18517 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 414 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8170 (tt0) cc_final: 0.7966 (tt0) REVERT: A 65 LYS cc_start: 0.8169 (mtpt) cc_final: 0.6399 (mtpt) REVERT: A 86 GLU cc_start: 0.7761 (pm20) cc_final: 0.7333 (pm20) REVERT: A 291 TYR cc_start: 0.8796 (p90) cc_final: 0.8481 (p90) REVERT: G 133 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8423 (tppt) REVERT: G 305 LYS cc_start: 0.8767 (tttt) cc_final: 0.8273 (mmpt) REVERT: G 319 TYR cc_start: 0.8713 (m-80) cc_final: 0.7717 (m-80) REVERT: F 54 ASN cc_start: 0.8291 (m-40) cc_final: 0.8071 (m-40) REVERT: B 53 ILE cc_start: 0.8931 (mm) cc_final: 0.8682 (mm) REVERT: B 137 LEU cc_start: 0.8901 (tp) cc_final: 0.8320 (tp) REVERT: B 141 MET cc_start: 0.8108 (ttt) cc_final: 0.7794 (tmm) REVERT: B 314 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.7383 (p) REVERT: E 61 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: E 82 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7470 (pt0) REVERT: E 98 TYR cc_start: 0.8684 (p90) cc_final: 0.8371 (p90) REVERT: E 122 ASP cc_start: 0.6693 (p0) cc_final: 0.6178 (p0) REVERT: E 126 ARG cc_start: 0.7830 (mtt-85) cc_final: 0.7398 (mmm160) REVERT: E 138 ASP cc_start: 0.8160 (m-30) cc_final: 0.7838 (t0) REVERT: E 170 GLN cc_start: 0.8464 (tp40) cc_final: 0.7895 (tp40) REVERT: E 236 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8379 (t0) REVERT: E 237 LYS cc_start: 0.7677 (tptt) cc_final: 0.7443 (tptt) REVERT: E 261 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8456 (mmmt) REVERT: C 152 THR cc_start: 0.8793 (m) cc_final: 0.8343 (p) REVERT: C 287 LEU cc_start: 0.8871 (mt) cc_final: 0.8566 (mt) REVERT: D 35 VAL cc_start: 0.8957 (t) cc_final: 0.8657 (m) REVERT: D 47 SER cc_start: 0.8944 (m) cc_final: 0.8682 (p) REVERT: D 175 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8400 (pt0) REVERT: D 208 TYR cc_start: 0.7630 (t80) cc_final: 0.7400 (t80) REVERT: D 224 ASP cc_start: 0.8145 (m-30) cc_final: 0.7799 (t0) REVERT: D 227 VAL cc_start: 0.8986 (t) cc_final: 0.8708 (p) outliers start: 71 outliers final: 48 residues processed: 456 average time/residue: 0.1583 time to fit residues: 103.8951 Evaluate side-chains 431 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 379 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 6 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 136 optimal weight: 30.0000 chunk 208 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 286 ASN ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS E 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104353 restraints weight = 37966.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.106719 restraints weight = 20264.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108306 restraints weight = 12402.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109384 restraints weight = 8341.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110171 restraints weight = 6003.409| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16965 Z= 0.170 Angle : 0.602 8.011 22985 Z= 0.319 Chirality : 0.046 0.204 2572 Planarity : 0.004 0.062 3063 Dihedral : 4.724 29.950 2377 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.46 % Allowed : 15.66 % Favored : 80.88 % 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 (0.18), residues: 2125 helix: 0.68 (0.22), residues: 556 sheet: -1.70 (0.23), residues: 416 loop : -1.15 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 231 TYR 0.018 0.002 TYR C 208 PHE 0.010 0.001 PHE E 49 TRP 0.012 0.002 TRP A 218 HIS 0.003 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00383 (16965) covalent geometry : angle 0.60206 (22985) hydrogen bonds : bond 0.04372 ( 660) hydrogen bonds : angle 6.02397 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 407 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8142 (tt0) cc_final: 0.7884 (tt0) REVERT: A 86 GLU cc_start: 0.7911 (pm20) cc_final: 0.7426 (pm20) REVERT: A 169 LEU cc_start: 0.8522 (mt) cc_final: 0.8317 (mt) REVERT: G 89 ASP cc_start: 0.7971 (t0) cc_final: 0.6712 (m-30) REVERT: G 133 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8400 (tppt) REVERT: G 160 MET cc_start: 0.8100 (pmm) cc_final: 0.7872 (pmm) REVERT: G 305 LYS cc_start: 0.8720 (tttt) cc_final: 0.8230 (mmpt) REVERT: G 319 TYR cc_start: 0.8657 (m-80) cc_final: 0.7543 (m-80) REVERT: G 326 CYS cc_start: 0.7333 (t) cc_final: 0.7076 (t) REVERT: F 98 TYR cc_start: 0.8181 (p90) cc_final: 0.7802 (p90) REVERT: F 283 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8119 (ptp-110) REVERT: B 53 ILE cc_start: 0.8931 (mm) cc_final: 0.8650 (mm) REVERT: B 93 MET cc_start: 0.8377 (mmt) cc_final: 0.7854 (mmt) REVERT: B 137 LEU cc_start: 0.8963 (tp) cc_final: 0.8537 (tp) REVERT: B 273 TYR cc_start: 0.8593 (m-80) cc_final: 0.8256 (m-80) REVERT: E 82 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7490 (pt0) REVERT: E 98 TYR cc_start: 0.8681 (p90) cc_final: 0.8319 (p90) REVERT: E 122 ASP cc_start: 0.6915 (p0) cc_final: 0.6337 (p0) REVERT: E 126 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.7394 (mmm160) REVERT: E 170 GLN cc_start: 0.8279 (tp40) cc_final: 0.7732 (tm-30) REVERT: E 236 ASP cc_start: 0.8665 (m-30) cc_final: 0.8295 (t0) REVERT: E 261 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8462 (mmmt) REVERT: C 152 THR cc_start: 0.8747 (m) cc_final: 0.8309 (p) REVERT: D 47 SER cc_start: 0.8996 (m) cc_final: 0.8754 (p) REVERT: D 51 LYS cc_start: 0.8576 (mmtp) cc_final: 0.8244 (mptt) REVERT: D 175 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: D 208 TYR cc_start: 0.7463 (t80) cc_final: 0.7256 (t80) REVERT: D 227 VAL cc_start: 0.8954 (t) cc_final: 0.8742 (p) REVERT: D 291 TYR cc_start: 0.8434 (p90) cc_final: 0.8070 (p90) outliers start: 61 outliers final: 46 residues processed: 443 average time/residue: 0.1545 time to fit residues: 98.2187 Evaluate side-chains 415 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 367 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 283 ARG Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 20 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN B 213 HIS B 311 ASN C 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102207 restraints weight = 38403.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.104572 restraints weight = 20660.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106171 restraints weight = 12733.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107195 restraints weight = 8618.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108007 restraints weight = 6300.645| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16965 Z= 0.204 Angle : 0.625 7.624 22985 Z= 0.331 Chirality : 0.046 0.158 2572 Planarity : 0.005 0.068 3063 Dihedral : 4.805 30.248 2377 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.25 % Allowed : 16.34 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.18), residues: 2125 helix: 0.54 (0.22), residues: 556 sheet: -1.76 (0.23), residues: 438 loop : -1.18 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 231 TYR 0.019 0.002 TYR B 312 PHE 0.033 0.002 PHE A 49 TRP 0.011 0.002 TRP B 117 HIS 0.004 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00465 (16965) covalent geometry : angle 0.62508 (22985) hydrogen bonds : bond 0.04455 ( 660) hydrogen bonds : angle 6.05617 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 398 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8160 (tt0) cc_final: 0.7902 (tt0) REVERT: A 86 GLU cc_start: 0.7969 (pm20) cc_final: 0.7431 (pm20) REVERT: G 35 VAL cc_start: 0.8548 (t) cc_final: 0.8306 (m) REVERT: G 89 ASP cc_start: 0.8002 (t0) cc_final: 0.6741 (m-30) REVERT: G 133 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8450 (tppt) REVERT: G 137 LEU cc_start: 0.8849 (tp) cc_final: 0.8515 (tt) REVERT: G 160 MET cc_start: 0.8173 (pmm) cc_final: 0.7926 (pmm) REVERT: G 299 THR cc_start: 0.8793 (m) cc_final: 0.8516 (p) REVERT: G 305 LYS cc_start: 0.8780 (tttt) cc_final: 0.8263 (mmpt) REVERT: G 319 TYR cc_start: 0.8673 (m-80) cc_final: 0.7479 (m-80) REVERT: F 54 ASN cc_start: 0.8308 (m-40) cc_final: 0.8107 (m-40) REVERT: F 98 TYR cc_start: 0.8109 (p90) cc_final: 0.7792 (p90) REVERT: F 283 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8107 (ptp-110) REVERT: B 53 ILE cc_start: 0.8943 (mm) cc_final: 0.8684 (mm) REVERT: B 261 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8318 (tppt) REVERT: B 273 TYR cc_start: 0.8464 (m-80) cc_final: 0.8123 (m-80) REVERT: B 290 TYR cc_start: 0.8016 (m-80) cc_final: 0.7479 (m-80) REVERT: B 331 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7418 (mm-30) REVERT: E 82 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7564 (pt0) REVERT: E 98 TYR cc_start: 0.8686 (p90) cc_final: 0.8290 (p90) REVERT: E 122 ASP cc_start: 0.7058 (p0) cc_final: 0.6397 (p0) REVERT: E 126 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7383 (mmm160) REVERT: E 170 GLN cc_start: 0.8257 (tp40) cc_final: 0.7754 (tm-30) REVERT: E 236 ASP cc_start: 0.8684 (m-30) cc_final: 0.8302 (t0) REVERT: E 261 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8486 (mmmt) REVERT: E 281 VAL cc_start: 0.9660 (t) cc_final: 0.9430 (p) REVERT: C 152 THR cc_start: 0.8734 (m) cc_final: 0.8322 (p) REVERT: D 47 SER cc_start: 0.9151 (m) cc_final: 0.8876 (p) REVERT: D 51 LYS cc_start: 0.8520 (mmtp) cc_final: 0.8216 (mttt) REVERT: D 56 TYR cc_start: 0.8320 (m-80) cc_final: 0.7894 (m-80) REVERT: D 208 TYR cc_start: 0.7564 (t80) cc_final: 0.7339 (t80) REVERT: D 227 VAL cc_start: 0.8950 (t) cc_final: 0.8673 (p) REVERT: D 291 TYR cc_start: 0.8564 (p90) cc_final: 0.8289 (p90) outliers start: 75 outliers final: 54 residues processed: 442 average time/residue: 0.1568 time to fit residues: 99.3300 Evaluate side-chains 429 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 374 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 94 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 283 ARG Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 154 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS C 124 GLN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.101148 restraints weight = 38381.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103478 restraints weight = 20609.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105054 restraints weight = 12741.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106120 restraints weight = 8659.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106898 restraints weight = 6305.932| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16965 Z= 0.229 Angle : 0.649 7.807 22985 Z= 0.344 Chirality : 0.047 0.186 2572 Planarity : 0.005 0.063 3063 Dihedral : 4.932 30.763 2377 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.54 % Allowed : 17.47 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2125 helix: 0.48 (0.22), residues: 552 sheet: -1.80 (0.23), residues: 450 loop : -1.19 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 99 TYR 0.020 0.002 TYR D 219 PHE 0.035 0.002 PHE A 49 TRP 0.012 0.002 TRP A 218 HIS 0.004 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00520 (16965) covalent geometry : angle 0.64852 (22985) hydrogen bonds : bond 0.04529 ( 660) hydrogen bonds : angle 6.13789 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 395 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7983 (pm20) cc_final: 0.7478 (pm20) REVERT: G 35 VAL cc_start: 0.8566 (t) cc_final: 0.8321 (m) REVERT: G 89 ASP cc_start: 0.8172 (t0) cc_final: 0.6808 (m-30) REVERT: G 133 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8452 (tppt) REVERT: G 160 MET cc_start: 0.8308 (pmm) cc_final: 0.8067 (pmm) REVERT: G 183 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: G 299 THR cc_start: 0.8794 (m) cc_final: 0.8567 (p) REVERT: G 302 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.6975 (t70) REVERT: G 305 LYS cc_start: 0.8791 (tttt) cc_final: 0.8262 (mmpt) REVERT: G 319 TYR cc_start: 0.8673 (m-80) cc_final: 0.7587 (m-80) REVERT: F 54 ASN cc_start: 0.8314 (m-40) cc_final: 0.8111 (m-40) REVERT: F 98 TYR cc_start: 0.8035 (p90) cc_final: 0.7732 (p90) REVERT: F 133 LYS cc_start: 0.8315 (ttpt) cc_final: 0.8096 (ptmt) REVERT: F 283 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8178 (ptp-110) REVERT: B 53 ILE cc_start: 0.8991 (mm) cc_final: 0.8740 (mm) REVERT: B 273 TYR cc_start: 0.8436 (m-80) cc_final: 0.8218 (m-80) REVERT: B 290 TYR cc_start: 0.8045 (m-80) cc_final: 0.7829 (m-80) REVERT: E 62 GLU cc_start: 0.8225 (tp30) cc_final: 0.7450 (tp30) REVERT: E 82 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7699 (pt0) REVERT: E 98 TYR cc_start: 0.8684 (p90) cc_final: 0.8309 (p90) REVERT: E 122 ASP cc_start: 0.7154 (p0) cc_final: 0.6537 (p0) REVERT: E 126 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7379 (mmm160) REVERT: E 170 GLN cc_start: 0.8251 (tp40) cc_final: 0.7630 (tm-30) REVERT: E 236 ASP cc_start: 0.8706 (m-30) cc_final: 0.8327 (t0) REVERT: E 261 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8492 (mmmt) REVERT: E 281 VAL cc_start: 0.9677 (t) cc_final: 0.9430 (p) REVERT: E 293 GLU cc_start: 0.7657 (tp30) cc_final: 0.7212 (mp0) REVERT: C 152 THR cc_start: 0.8756 (m) cc_final: 0.8368 (p) REVERT: C 287 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8734 (mt) REVERT: C 290 TYR cc_start: 0.7661 (m-10) cc_final: 0.7437 (m-10) REVERT: D 47 SER cc_start: 0.9280 (m) cc_final: 0.8999 (p) REVERT: D 51 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8309 (mttt) REVERT: D 56 TYR cc_start: 0.8388 (m-80) cc_final: 0.7842 (m-80) REVERT: D 137 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8779 (tt) REVERT: D 227 VAL cc_start: 0.8968 (t) cc_final: 0.8714 (p) outliers start: 80 outliers final: 61 residues processed: 440 average time/residue: 0.1525 time to fit residues: 96.1069 Evaluate side-chains 435 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 369 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 283 ARG Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 117 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 209 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 GLN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099973 restraints weight = 38730.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102268 restraints weight = 20851.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.103825 restraints weight = 12925.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104890 restraints weight = 8793.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105675 restraints weight = 6392.380| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 16965 Z= 0.272 Angle : 0.701 8.809 22985 Z= 0.370 Chirality : 0.048 0.187 2572 Planarity : 0.005 0.066 3063 Dihedral : 5.161 31.161 2377 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.54 % Allowed : 18.38 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.18), residues: 2125 helix: 0.27 (0.22), residues: 557 sheet: -1.94 (0.23), residues: 443 loop : -1.18 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 99 TYR 0.023 0.002 TYR D 219 PHE 0.032 0.002 PHE E 49 TRP 0.013 0.002 TRP C 117 HIS 0.006 0.002 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00620 (16965) covalent geometry : angle 0.70080 (22985) hydrogen bonds : bond 0.04726 ( 660) hydrogen bonds : angle 6.29161 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 378 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8321 (tt0) cc_final: 0.7979 (tt0) REVERT: A 86 GLU cc_start: 0.8012 (pm20) cc_final: 0.7472 (pm20) REVERT: A 124 GLN cc_start: 0.8974 (tp40) cc_final: 0.8731 (tp40) REVERT: A 155 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6843 (mmt90) REVERT: G 35 VAL cc_start: 0.8659 (t) cc_final: 0.8399 (m) REVERT: G 89 ASP cc_start: 0.8040 (t0) cc_final: 0.6693 (m-30) REVERT: G 133 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8451 (tppt) REVERT: G 183 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: G 221 GLU cc_start: 0.8046 (pm20) cc_final: 0.7793 (pm20) REVERT: G 299 THR cc_start: 0.8848 (m) cc_final: 0.8612 (p) REVERT: G 302 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7011 (t70) REVERT: G 305 LYS cc_start: 0.8818 (tttt) cc_final: 0.8477 (mmpt) REVERT: G 319 TYR cc_start: 0.8693 (m-80) cc_final: 0.7808 (m-80) REVERT: F 98 TYR cc_start: 0.8056 (p90) cc_final: 0.7766 (p90) REVERT: F 283 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8121 (ptp-110) REVERT: B 53 ILE cc_start: 0.9014 (mm) cc_final: 0.8770 (mm) REVERT: B 181 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7803 (mtt) REVERT: B 273 TYR cc_start: 0.8427 (m-80) cc_final: 0.8175 (m-80) REVERT: E 82 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7620 (pt0) REVERT: E 98 TYR cc_start: 0.8705 (p90) cc_final: 0.8391 (p90) REVERT: E 122 ASP cc_start: 0.7258 (p0) cc_final: 0.6718 (p0) REVERT: E 126 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7416 (mmm160) REVERT: E 170 GLN cc_start: 0.8252 (tp40) cc_final: 0.7737 (tm-30) REVERT: E 236 ASP cc_start: 0.8724 (m-30) cc_final: 0.8339 (t0) REVERT: E 261 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8443 (mmmt) REVERT: E 281 VAL cc_start: 0.9689 (t) cc_final: 0.9443 (p) REVERT: E 291 TYR cc_start: 0.8658 (p90) cc_final: 0.8417 (p90) REVERT: E 293 GLU cc_start: 0.7711 (tp30) cc_final: 0.6928 (mp0) REVERT: C 51 LYS cc_start: 0.8810 (mttp) cc_final: 0.8605 (mttp) REVERT: C 152 THR cc_start: 0.8777 (m) cc_final: 0.8374 (p) REVERT: C 273 TYR cc_start: 0.8395 (m-80) cc_final: 0.8145 (m-80) REVERT: C 287 LEU cc_start: 0.8954 (mt) cc_final: 0.8740 (mt) REVERT: D 47 SER cc_start: 0.9228 (m) cc_final: 0.9027 (p) REVERT: D 49 PHE cc_start: 0.8571 (t80) cc_final: 0.8369 (t80) REVERT: D 56 TYR cc_start: 0.8335 (m-80) cc_final: 0.7899 (m-80) REVERT: D 137 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8775 (tt) REVERT: D 227 VAL cc_start: 0.8990 (t) cc_final: 0.8775 (p) outliers start: 80 outliers final: 60 residues processed: 425 average time/residue: 0.1480 time to fit residues: 91.1732 Evaluate side-chains 413 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 283 ARG Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 165 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 122 optimal weight: 0.1980 chunk 7 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN C 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.108922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099775 restraints weight = 39110.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102082 restraints weight = 20988.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103653 restraints weight = 12973.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104735 restraints weight = 8820.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105459 restraints weight = 6402.432| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 16965 Z= 0.260 Angle : 0.704 8.018 22985 Z= 0.372 Chirality : 0.048 0.189 2572 Planarity : 0.005 0.069 3063 Dihedral : 5.192 31.300 2377 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.59 % Allowed : 19.46 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.18), residues: 2125 helix: 0.25 (0.22), residues: 558 sheet: -2.00 (0.23), residues: 438 loop : -1.24 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 99 TYR 0.022 0.002 TYR D 219 PHE 0.028 0.002 PHE E 49 TRP 0.012 0.002 TRP C 117 HIS 0.005 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00593 (16965) covalent geometry : angle 0.70408 (22985) hydrogen bonds : bond 0.04728 ( 660) hydrogen bonds : angle 6.30311 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 363 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLN cc_start: 0.8959 (tp40) cc_final: 0.8750 (tp40) REVERT: A 149 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7253 (tpp80) REVERT: A 155 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6831 (mmt90) REVERT: A 322 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7789 (pt0) REVERT: G 35 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8410 (m) REVERT: G 89 ASP cc_start: 0.7913 (t0) cc_final: 0.6550 (m-30) REVERT: G 133 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8400 (tppt) REVERT: G 137 LEU cc_start: 0.8863 (tp) cc_final: 0.8655 (tt) REVERT: G 183 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: G 221 GLU cc_start: 0.8012 (pm20) cc_final: 0.7789 (pm20) REVERT: G 299 THR cc_start: 0.8858 (m) cc_final: 0.8629 (p) REVERT: G 302 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.6997 (t70) REVERT: G 305 LYS cc_start: 0.8719 (tttt) cc_final: 0.8441 (mmpt) REVERT: G 319 TYR cc_start: 0.8668 (m-80) cc_final: 0.7678 (m-80) REVERT: F 98 TYR cc_start: 0.7960 (p90) cc_final: 0.7715 (p90) REVERT: F 283 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8187 (ptp-110) REVERT: B 53 ILE cc_start: 0.9020 (mm) cc_final: 0.8784 (mm) REVERT: B 181 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7867 (mtt) REVERT: B 273 TYR cc_start: 0.8366 (m-80) cc_final: 0.8138 (m-80) REVERT: B 290 TYR cc_start: 0.8129 (m-80) cc_final: 0.7564 (m-80) REVERT: E 56 TYR cc_start: 0.6651 (m-10) cc_final: 0.6352 (m-10) REVERT: E 82 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7658 (pt0) REVERT: E 98 TYR cc_start: 0.8672 (p90) cc_final: 0.8330 (p90) REVERT: E 122 ASP cc_start: 0.7264 (p0) cc_final: 0.6787 (p0) REVERT: E 126 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7462 (mmm160) REVERT: E 170 GLN cc_start: 0.8204 (tp40) cc_final: 0.7818 (tm-30) REVERT: E 236 ASP cc_start: 0.8722 (m-30) cc_final: 0.8334 (t0) REVERT: E 261 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8447 (mmmt) REVERT: E 281 VAL cc_start: 0.9685 (t) cc_final: 0.9444 (p) REVERT: E 291 TYR cc_start: 0.8614 (p90) cc_final: 0.7443 (p90) REVERT: E 293 GLU cc_start: 0.7810 (tp30) cc_final: 0.6595 (mp0) REVERT: C 152 THR cc_start: 0.8787 (m) cc_final: 0.8386 (p) REVERT: C 287 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8704 (mt) REVERT: D 56 TYR cc_start: 0.8343 (m-80) cc_final: 0.7933 (m-80) REVERT: D 137 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8760 (tt) REVERT: D 227 VAL cc_start: 0.9034 (t) cc_final: 0.8758 (p) REVERT: D 261 LYS cc_start: 0.8628 (tppt) cc_final: 0.8200 (tttt) outliers start: 81 outliers final: 65 residues processed: 408 average time/residue: 0.1472 time to fit residues: 87.2120 Evaluate side-chains 426 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 352 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain G residue 302 ASP Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 283 ARG Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 84 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN D 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103549 restraints weight = 38205.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105881 restraints weight = 20380.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107449 restraints weight = 12506.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108545 restraints weight = 8445.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109316 restraints weight = 6076.845| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16965 Z= 0.146 Angle : 0.621 7.884 22985 Z= 0.330 Chirality : 0.046 0.178 2572 Planarity : 0.004 0.067 3063 Dihedral : 4.860 28.794 2377 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.46 % Allowed : 20.53 % Favored : 76.01 % 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: -1.35 (0.18), residues: 2125 helix: 0.42 (0.22), residues: 568 sheet: -1.80 (0.24), residues: 405 loop : -1.20 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 99 TYR 0.020 0.002 TYR D 208 PHE 0.038 0.002 PHE E 49 TRP 0.010 0.001 TRP A 218 HIS 0.003 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00326 (16965) covalent geometry : angle 0.62054 (22985) hydrogen bonds : bond 0.04323 ( 660) hydrogen bonds : angle 6.03126 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 395 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8213 (tt0) cc_final: 0.7952 (tt0) REVERT: A 86 GLU cc_start: 0.8091 (pm20) cc_final: 0.7517 (pm20) REVERT: A 124 GLN cc_start: 0.8892 (tp40) cc_final: 0.8615 (tp40) REVERT: G 35 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8378 (m) REVERT: G 89 ASP cc_start: 0.7776 (t0) cc_final: 0.6582 (m-30) REVERT: G 133 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8450 (tppt) REVERT: G 183 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: G 221 GLU cc_start: 0.8030 (pm20) cc_final: 0.7792 (pm20) REVERT: G 299 THR cc_start: 0.8759 (m) cc_final: 0.8552 (p) REVERT: G 302 ASP cc_start: 0.7500 (m-30) cc_final: 0.6894 (t70) REVERT: G 305 LYS cc_start: 0.8382 (tttt) cc_final: 0.8106 (mmpt) REVERT: G 319 TYR cc_start: 0.8495 (m-80) cc_final: 0.7678 (m-80) REVERT: F 283 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8069 (ptp-110) REVERT: B 53 ILE cc_start: 0.8952 (mm) cc_final: 0.8643 (mm) REVERT: B 169 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8253 (tp) REVERT: B 181 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7735 (mtt) REVERT: E 56 TYR cc_start: 0.6463 (m-10) cc_final: 0.6140 (m-10) REVERT: E 82 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7706 (pt0) REVERT: E 98 TYR cc_start: 0.8631 (p90) cc_final: 0.8263 (p90) REVERT: E 122 ASP cc_start: 0.7134 (p0) cc_final: 0.6677 (p0) REVERT: E 126 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.7507 (mmm160) REVERT: E 170 GLN cc_start: 0.7965 (tp40) cc_final: 0.7736 (tm-30) REVERT: E 236 ASP cc_start: 0.8636 (m-30) cc_final: 0.8254 (t0) REVERT: E 261 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8461 (mmmt) REVERT: E 281 VAL cc_start: 0.9691 (t) cc_final: 0.9438 (p) REVERT: E 296 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7519 (ttp-110) REVERT: C 51 LYS cc_start: 0.8822 (mttp) cc_final: 0.8282 (mptt) REVERT: C 152 THR cc_start: 0.8742 (m) cc_final: 0.8315 (p) REVERT: C 287 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8629 (mt) REVERT: D 56 TYR cc_start: 0.8290 (m-80) cc_final: 0.7872 (m-80) REVERT: D 227 VAL cc_start: 0.9018 (t) cc_final: 0.8767 (p) REVERT: D 261 LYS cc_start: 0.8392 (tppt) cc_final: 0.8167 (tttt) outliers start: 61 outliers final: 44 residues processed: 429 average time/residue: 0.1532 time to fit residues: 95.1790 Evaluate side-chains 423 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 373 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 283 ARG Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 329 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 125 optimal weight: 0.0470 chunk 167 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 194 optimal weight: 0.0470 chunk 148 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 overall best weight: 3.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS E 311 ASN C 124 GLN C 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.103277 restraints weight = 38294.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105588 restraints weight = 20377.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107141 restraints weight = 12483.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108226 restraints weight = 8428.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108997 restraints weight = 6065.434| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16965 Z= 0.169 Angle : 0.658 8.660 22985 Z= 0.348 Chirality : 0.047 0.238 2572 Planarity : 0.005 0.070 3063 Dihedral : 4.876 28.108 2377 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.95 % Allowed : 21.55 % 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: -1.30 (0.18), residues: 2125 helix: 0.46 (0.22), residues: 568 sheet: -1.76 (0.24), residues: 401 loop : -1.17 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 139 TYR 0.037 0.002 TYR C 56 PHE 0.042 0.002 PHE E 49 TRP 0.017 0.002 TRP E 117 HIS 0.003 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00389 (16965) covalent geometry : angle 0.65759 (22985) hydrogen bonds : bond 0.04353 ( 660) hydrogen bonds : angle 6.04422 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4250 Ramachandran restraints generated. 2125 Oldfield, 0 Emsley, 2125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 377 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8353 (tt0) cc_final: 0.7951 (tt0) REVERT: A 86 GLU cc_start: 0.8024 (pm20) cc_final: 0.7503 (pm20) REVERT: A 124 GLN cc_start: 0.8901 (tp40) cc_final: 0.8623 (tp40) REVERT: A 155 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6866 (mmt90) REVERT: G 35 VAL cc_start: 0.8644 (t) cc_final: 0.8335 (m) REVERT: G 89 ASP cc_start: 0.7818 (t0) cc_final: 0.6614 (m-30) REVERT: G 133 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8458 (tppt) REVERT: G 183 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: G 299 THR cc_start: 0.8762 (m) cc_final: 0.8557 (p) REVERT: G 302 ASP cc_start: 0.7524 (m-30) cc_final: 0.6929 (t70) REVERT: G 305 LYS cc_start: 0.8383 (tttt) cc_final: 0.8104 (mmpt) REVERT: G 319 TYR cc_start: 0.8504 (m-80) cc_final: 0.7576 (m-80) REVERT: F 283 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8053 (ptp-110) REVERT: B 53 ILE cc_start: 0.8908 (mm) cc_final: 0.8652 (mm) REVERT: B 85 ARG cc_start: 0.6138 (ttt180) cc_final: 0.5722 (mtm180) REVERT: B 181 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7743 (mtt) REVERT: B 213 HIS cc_start: 0.7948 (m-70) cc_final: 0.7301 (m170) REVERT: B 238 TYR cc_start: 0.7137 (m-80) cc_final: 0.6841 (m-80) REVERT: B 290 TYR cc_start: 0.7776 (m-80) cc_final: 0.7341 (m-80) REVERT: E 56 TYR cc_start: 0.6157 (m-10) cc_final: 0.5879 (m-10) REVERT: E 82 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7680 (pt0) REVERT: E 122 ASP cc_start: 0.7143 (p0) cc_final: 0.6682 (p0) REVERT: E 126 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7472 (mmm160) REVERT: E 170 GLN cc_start: 0.7966 (tp40) cc_final: 0.7739 (tm-30) REVERT: E 236 ASP cc_start: 0.8635 (m-30) cc_final: 0.8270 (t0) REVERT: E 261 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8451 (mmmt) REVERT: E 281 VAL cc_start: 0.9690 (t) cc_final: 0.9446 (p) REVERT: C 51 LYS cc_start: 0.8773 (mttp) cc_final: 0.8244 (mptt) REVERT: C 152 THR cc_start: 0.8734 (m) cc_final: 0.8312 (p) REVERT: C 287 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8700 (mt) REVERT: D 56 TYR cc_start: 0.8268 (m-80) cc_final: 0.7886 (m-80) REVERT: D 142 ILE cc_start: 0.8769 (tt) cc_final: 0.8546 (pt) REVERT: D 227 VAL cc_start: 0.8992 (t) cc_final: 0.8720 (p) REVERT: D 261 LYS cc_start: 0.8435 (tppt) cc_final: 0.8217 (tttt) outliers start: 52 outliers final: 40 residues processed: 407 average time/residue: 0.1535 time to fit residues: 89.9888 Evaluate side-chains 410 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 365 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 300 ILE Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 283 ARG Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 329 MET Chi-restraints excluded: chain D residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 91 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** G 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN C 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101948 restraints weight = 38499.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.104264 restraints weight = 20604.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105850 restraints weight = 12672.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106920 restraints weight = 8557.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107693 restraints weight = 6190.886| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 16965 Z= 0.225 Angle : 0.684 9.566 22985 Z= 0.361 Chirality : 0.048 0.198 2572 Planarity : 0.005 0.088 3063 Dihedral : 4.946 28.379 2377 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.18 % Allowed : 21.84 % Favored : 74.99 % 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: -1.40 (0.18), residues: 2125 helix: 0.32 (0.22), residues: 577 sheet: -1.85 (0.23), residues: 412 loop : -1.18 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 99 TYR 0.031 0.002 TYR C 56 PHE 0.040 0.002 PHE E 49 TRP 0.011 0.002 TRP A 218 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00518 (16965) covalent geometry : angle 0.68450 (22985) hydrogen bonds : bond 0.04507 ( 660) hydrogen bonds : angle 6.09022 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3715.05 seconds wall clock time: 64 minutes 52.40 seconds (3892.40 seconds total)