Starting phenix.real_space_refine on Wed Mar 4 08:48:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t90_25749/03_2026/7t90_25749_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t90_25749/03_2026/7t90_25749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t90_25749/03_2026/7t90_25749_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t90_25749/03_2026/7t90_25749_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t90_25749/03_2026/7t90_25749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t90_25749/03_2026/7t90_25749.map" } resolution = 3.32 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= -0.004 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4680 atoms to isotropic. 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 58 5.16 5 C 5384 2.51 5 N 1431 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8451 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2042 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 276, 2028 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 79 Conformer: "B" Number of residues, atoms: 276, 2028 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 79 bond proxies already assigned to first conformer: 2063 Chain: "B" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1707 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2541 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1747 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 427 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 427 " occ=0.50 Time building chain proxies: 2.40, per 1000 atoms: 0.28 Number of scatterers: 8451 At special positions: 0 Unit cell: (90.95, 122.4, 125.8, 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 58 16.00 O 1578 8.00 N 1431 7.00 C 5384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 385.3 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.3% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 22 through 51 removed outlier: 3.949A pdb=" N ILE A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 87 removed outlier: 3.898A pdb=" N SER A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 127 removed outlier: 4.224A pdb=" N VAL A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 136 through 162 Proline residue: A 157 - end of helix removed outlier: 3.629A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.514A pdb=" N PHE A 181 " --> pdb=" O ILE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 214 removed outlier: 3.693A pdb=" N THR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Proline residue: A 198 - end of helix removed outlier: 4.037A pdb=" N LYS A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 413 removed outlier: 3.706A pdb=" N ALA A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Proline residue: A 402 - end of helix removed outlier: 3.937A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 removed outlier: 4.279A pdb=" N CYS A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.855A pdb=" N LYS A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.543A pdb=" N GLU B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.749A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.650A pdb=" N LYS B 211 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.575A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 329 through 351 removed outlier: 4.014A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.277A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.874A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.966A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.757A pdb=" N ASP B 201 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 38 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N ALA B 221 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.527A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.699A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 103 through 105 removed outlier: 3.550A pdb=" N ALA C 113 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 112 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.918A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.559A pdb=" N SER C 191 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 200 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.529A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.159A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.549A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.125A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.887A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.993A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.076A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.822A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1366 1.31 - 1.43: 2406 1.43 - 1.56: 4775 1.56 - 1.69: 0 1.69 - 1.82: 82 Bond restraints: 8629 Sorted by residual: bond pdb=" C2 ACH A 501 " pdb=" N1 ACH A 501 " ideal model delta sigma weight residual 1.506 1.421 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" CA ILE A 165 " pdb=" CB ILE A 165 " ideal model delta sigma weight residual 1.540 1.486 0.054 1.36e-02 5.41e+03 1.60e+01 bond pdb=" CA SER A 433 " pdb=" CB SER A 433 " ideal model delta sigma weight residual 1.528 1.470 0.059 1.56e-02 4.11e+03 1.41e+01 bond pdb=" C TRP A 422 " pdb=" O TRP A 422 " ideal model delta sigma weight residual 1.236 1.279 -0.042 1.15e-02 7.56e+03 1.36e+01 bond pdb=" N ILE A 217 " pdb=" CA ILE A 217 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.22e-02 6.72e+03 1.29e+01 ... (remaining 8624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 11471 2.72 - 5.45: 233 5.45 - 8.17: 27 8.17 - 10.90: 9 10.90 - 13.62: 4 Bond angle restraints: 11744 Sorted by residual: angle pdb=" N THR A 170 " pdb=" CA THR A 170 " pdb=" C THR A 170 " ideal model delta sigma weight residual 112.90 99.28 13.62 1.31e+00 5.83e-01 1.08e+02 angle pdb=" N ASN A 419 " pdb=" CA ASN A 419 " pdb=" C ASN A 419 " ideal model delta sigma weight residual 113.19 101.58 11.61 1.19e+00 7.06e-01 9.52e+01 angle pdb=" N LEU A 82 " pdb=" CA LEU A 82 " pdb=" C LEU A 82 " ideal model delta sigma weight residual 111.28 102.19 9.09 1.09e+00 8.42e-01 6.95e+01 angle pdb=" N SER A 182 " pdb=" CA SER A 182 " pdb=" C SER A 182 " ideal model delta sigma weight residual 112.88 104.64 8.24 1.29e+00 6.01e-01 4.08e+01 angle pdb=" C PRO A 437 " pdb=" CA PRO A 437 " pdb=" CB PRO A 437 " ideal model delta sigma weight residual 113.06 103.26 9.80 1.59e+00 3.96e-01 3.80e+01 ... (remaining 11739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4640 17.93 - 35.86: 343 35.86 - 53.80: 65 53.80 - 71.73: 4 71.73 - 89.66: 1 Dihedral angle restraints: 5053 sinusoidal: 1795 harmonic: 3258 Sorted by residual: dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 176 " pdb=" CB CYS A 176 " ideal model delta sinusoidal sigma weight residual 93.00 43.05 49.95 1 1.00e+01 1.00e-02 3.42e+01 dihedral pdb=" CA HIS C 225 " pdb=" C HIS C 225 " pdb=" N GLU C 226 " pdb=" CA GLU C 226 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1188 0.083 - 0.166: 144 0.166 - 0.249: 15 0.249 - 0.332: 11 0.332 - 0.415: 6 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CA ASN A 183 " pdb=" N ASN A 183 " pdb=" C ASN A 183 " pdb=" CB ASN A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CB ILE A 72 " pdb=" CA ILE A 72 " pdb=" CG1 ILE A 72 " pdb=" CG2 ILE A 72 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA LEU A 82 " pdb=" N LEU A 82 " pdb=" C LEU A 82 " pdb=" CB LEU A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 1361 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BTRP A 427 " -0.024 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C BTRP A 427 " 0.087 2.00e-02 2.50e+03 pdb=" O BTRP A 427 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU A 428 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 163 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLN A 163 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN A 163 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE A 164 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 408 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C LEU A 408 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A 408 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE A 409 " -0.021 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 265 2.70 - 3.25: 8232 3.25 - 3.80: 12611 3.80 - 4.35: 16056 4.35 - 4.90: 27493 Nonbonded interactions: 64657 Sorted by model distance: nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.146 3.040 nonbonded pdb=" O LEU A 43 " pdb=" OG SER A 47 " model vdw 2.162 3.040 nonbonded pdb=" ND2 ASN C 119 " pdb=" O GLY C 144 " model vdw 2.190 3.120 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.226 3.040 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.228 3.040 ... (remaining 64652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 8632 Z= 0.355 Angle : 0.945 13.621 11750 Z= 0.628 Chirality : 0.063 0.415 1364 Planarity : 0.005 0.050 1483 Dihedral : 12.713 89.660 2944 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.23 % Allowed : 0.92 % Favored : 98.85 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 1107 helix: 1.79 (0.29), residues: 337 sheet: -1.36 (0.33), residues: 262 loop : -1.64 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 98 TYR 0.021 0.002 TYR A 426 PHE 0.015 0.001 PHE C 235 TRP 0.012 0.001 TRP E 47 HIS 0.006 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 8629) covalent geometry : angle 0.94539 (11744) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.03421 ( 6) hydrogen bonds : bond 0.21072 ( 382) hydrogen bonds : angle 7.41985 ( 1075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.5377 (mmt) cc_final: 0.5110 (mmt) REVERT: A 444 ASN cc_start: 0.8528 (t0) cc_final: 0.8098 (t0) REVERT: B 187 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7979 (tm-30) REVERT: B 246 GLU cc_start: 0.7636 (tt0) cc_final: 0.7152 (mt-10) REVERT: E 38 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7818 (ptt180) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.0854 time to fit residues: 21.7621 Evaluate side-chains 130 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 108 ASN A 436 ASN E 35 HIS E 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104903 restraints weight = 29776.488| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.08 r_work: 0.3292 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8632 Z= 0.166 Angle : 0.630 9.265 11750 Z= 0.339 Chirality : 0.045 0.227 1364 Planarity : 0.004 0.037 1483 Dihedral : 4.784 32.428 1205 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.62 % Allowed : 9.12 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.26), residues: 1107 helix: 2.03 (0.28), residues: 354 sheet: -1.19 (0.32), residues: 264 loop : -1.53 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.018 0.002 TYR E 94 PHE 0.010 0.001 PHE C 235 TRP 0.013 0.001 TRP C 82 HIS 0.006 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8629) covalent geometry : angle 0.63007 (11744) SS BOND : bond 0.00457 ( 3) SS BOND : angle 0.91481 ( 6) hydrogen bonds : bond 0.05224 ( 382) hydrogen bonds : angle 5.27250 ( 1075) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7847 (tm-30) REVERT: B 246 GLU cc_start: 0.8056 (tt0) cc_final: 0.7462 (mt-10) REVERT: D 47 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: E 38 ARG cc_start: 0.8451 (ptt90) cc_final: 0.8114 (ptt180) REVERT: E 82 GLN cc_start: 0.6383 (mm110) cc_final: 0.5861 (mp10) REVERT: E 156 SER cc_start: 0.8564 (t) cc_final: 0.8348 (m) outliers start: 14 outliers final: 7 residues processed: 151 average time/residue: 0.0767 time to fit residues: 16.9263 Evaluate side-chains 133 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.0010 chunk 105 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.0670 chunk 48 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN E 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.137828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107288 restraints weight = 31194.109| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.62 r_work: 0.3306 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8632 Z= 0.120 Angle : 0.561 9.321 11750 Z= 0.300 Chirality : 0.043 0.180 1364 Planarity : 0.004 0.036 1483 Dihedral : 4.298 19.707 1205 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.62 % Allowed : 13.05 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1107 helix: 2.30 (0.28), residues: 355 sheet: -0.85 (0.33), residues: 263 loop : -1.39 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 251 TYR 0.017 0.001 TYR E 190 PHE 0.011 0.001 PHE A 451 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8629) covalent geometry : angle 0.56031 (11744) SS BOND : bond 0.00401 ( 3) SS BOND : angle 0.85557 ( 6) hydrogen bonds : bond 0.04172 ( 382) hydrogen bonds : angle 4.66475 ( 1075) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: B 246 GLU cc_start: 0.8040 (tt0) cc_final: 0.7459 (mt-10) REVERT: E 82 GLN cc_start: 0.6118 (mm110) cc_final: 0.5780 (mp10) outliers start: 14 outliers final: 8 residues processed: 149 average time/residue: 0.0774 time to fit residues: 16.7586 Evaluate side-chains 134 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 99 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.136127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105593 restraints weight = 30083.221| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 4.13 r_work: 0.3293 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8632 Z= 0.136 Angle : 0.561 9.447 11750 Z= 0.302 Chirality : 0.043 0.171 1364 Planarity : 0.003 0.037 1483 Dihedral : 4.263 21.222 1205 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.85 % Allowed : 14.32 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1107 helix: 2.45 (0.28), residues: 353 sheet: -0.92 (0.32), residues: 272 loop : -1.20 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.018 0.001 TYR E 190 PHE 0.010 0.001 PHE C 235 TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8629) covalent geometry : angle 0.56076 (11744) SS BOND : bond 0.00498 ( 3) SS BOND : angle 0.90912 ( 6) hydrogen bonds : bond 0.04121 ( 382) hydrogen bonds : angle 4.52049 ( 1075) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 436 ASN cc_start: 0.7143 (OUTLIER) cc_final: 0.6865 (m110) REVERT: B 43 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7872 (tm-30) REVERT: B 246 GLU cc_start: 0.8079 (tt0) cc_final: 0.7483 (mt-10) REVERT: E 82 GLN cc_start: 0.6173 (mm110) cc_final: 0.5853 (mp10) outliers start: 16 outliers final: 12 residues processed: 139 average time/residue: 0.0699 time to fit residues: 14.4132 Evaluate side-chains 134 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.136800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108788 restraints weight = 26184.719| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.35 r_work: 0.3292 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8632 Z= 0.117 Angle : 0.543 9.828 11750 Z= 0.288 Chirality : 0.042 0.166 1364 Planarity : 0.003 0.036 1483 Dihedral : 4.141 18.696 1205 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.85 % Allowed : 14.55 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1107 helix: 2.54 (0.28), residues: 354 sheet: -0.73 (0.32), residues: 266 loop : -1.18 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.016 0.001 TYR E 190 PHE 0.009 0.001 PHE A 451 TRP 0.011 0.001 TRP C 82 HIS 0.006 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8629) covalent geometry : angle 0.54273 (11744) SS BOND : bond 0.00434 ( 3) SS BOND : angle 0.72177 ( 6) hydrogen bonds : bond 0.03849 ( 382) hydrogen bonds : angle 4.40086 ( 1075) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 226 VAL cc_start: 0.9422 (OUTLIER) cc_final: 0.9142 (m) REVERT: B 246 GLU cc_start: 0.8098 (tt0) cc_final: 0.7498 (mt-10) REVERT: C 220 GLN cc_start: 0.8097 (mt0) cc_final: 0.7826 (mt0) REVERT: E 82 GLN cc_start: 0.6084 (mm110) cc_final: 0.5756 (mp10) outliers start: 16 outliers final: 12 residues processed: 136 average time/residue: 0.0780 time to fit residues: 15.5553 Evaluate side-chains 134 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 99 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.0270 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 13 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.138989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110734 restraints weight = 26475.739| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 4.44 r_work: 0.3320 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 8632 Z= 0.107 Angle : 0.525 9.686 11750 Z= 0.278 Chirality : 0.042 0.164 1364 Planarity : 0.003 0.035 1483 Dihedral : 3.940 17.229 1205 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.85 % Allowed : 15.70 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1107 helix: 2.63 (0.28), residues: 354 sheet: -0.53 (0.33), residues: 255 loop : -1.09 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.015 0.001 TYR E 190 PHE 0.011 0.001 PHE C 335 TRP 0.011 0.001 TRP C 82 HIS 0.005 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8629) covalent geometry : angle 0.52455 (11744) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.61295 ( 6) hydrogen bonds : bond 0.03458 ( 382) hydrogen bonds : angle 4.20046 ( 1075) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: B 226 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9166 (m) REVERT: B 246 GLU cc_start: 0.8064 (tt0) cc_final: 0.7472 (mt-10) REVERT: C 220 GLN cc_start: 0.8008 (mt0) cc_final: 0.7735 (mt0) REVERT: E 82 GLN cc_start: 0.6036 (mm110) cc_final: 0.5677 (mp10) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 0.0742 time to fit residues: 15.7201 Evaluate side-chains 146 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 140 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106067 restraints weight = 29851.804| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.16 r_work: 0.3311 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 8632 Z= 0.124 Angle : 0.539 10.058 11750 Z= 0.288 Chirality : 0.042 0.171 1364 Planarity : 0.003 0.038 1483 Dihedral : 4.009 17.478 1205 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.31 % Allowed : 15.47 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 1107 helix: 2.66 (0.28), residues: 354 sheet: -0.48 (0.33), residues: 256 loop : -1.05 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.017 0.001 TYR B 303 PHE 0.008 0.001 PHE A 451 TRP 0.010 0.001 TRP C 82 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8629) covalent geometry : angle 0.53909 (11744) SS BOND : bond 0.00437 ( 3) SS BOND : angle 0.73663 ( 6) hydrogen bonds : bond 0.03678 ( 382) hydrogen bonds : angle 4.21708 ( 1075) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6221 (mpp) REVERT: B 226 VAL cc_start: 0.9428 (OUTLIER) cc_final: 0.9165 (m) REVERT: B 246 GLU cc_start: 0.8083 (tt0) cc_final: 0.7445 (mt-10) REVERT: C 220 GLN cc_start: 0.8035 (mt0) cc_final: 0.7776 (mt0) REVERT: E 82 GLN cc_start: 0.6107 (mm110) cc_final: 0.5745 (mp10) outliers start: 20 outliers final: 15 residues processed: 138 average time/residue: 0.0680 time to fit residues: 13.9587 Evaluate side-chains 140 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 140 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 14 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107127 restraints weight = 30008.557| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 4.18 r_work: 0.3298 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 8632 Z= 0.131 Angle : 0.554 10.415 11750 Z= 0.294 Chirality : 0.043 0.166 1364 Planarity : 0.003 0.037 1483 Dihedral : 4.079 17.922 1205 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.96 % Allowed : 16.40 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1107 helix: 2.62 (0.28), residues: 355 sheet: -0.48 (0.33), residues: 256 loop : -0.98 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.015 0.001 TYR E 190 PHE 0.012 0.001 PHE C 335 TRP 0.009 0.001 TRP C 82 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8629) covalent geometry : angle 0.55343 (11744) SS BOND : bond 0.00473 ( 3) SS BOND : angle 0.75736 ( 6) hydrogen bonds : bond 0.03780 ( 382) hydrogen bonds : angle 4.22865 ( 1075) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6264 (mpp) REVERT: B 246 GLU cc_start: 0.8095 (tt0) cc_final: 0.7435 (mt-10) REVERT: C 220 GLN cc_start: 0.8006 (mt0) cc_final: 0.7747 (mt0) REVERT: E 82 GLN cc_start: 0.6113 (mm110) cc_final: 0.5748 (mp10) outliers start: 17 outliers final: 14 residues processed: 136 average time/residue: 0.0753 time to fit residues: 15.1495 Evaluate side-chains 140 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.136271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106589 restraints weight = 34002.401| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 4.39 r_work: 0.3295 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 8632 Z= 0.137 Angle : 0.558 10.254 11750 Z= 0.298 Chirality : 0.043 0.179 1364 Planarity : 0.003 0.037 1483 Dihedral : 4.125 18.249 1205 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.42 % Allowed : 16.17 % Favored : 81.41 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1107 helix: 2.61 (0.28), residues: 354 sheet: -0.47 (0.33), residues: 256 loop : -0.97 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.030 0.001 TYR B 303 PHE 0.007 0.001 PHE C 235 TRP 0.009 0.001 TRP C 82 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8629) covalent geometry : angle 0.55782 (11744) SS BOND : bond 0.00497 ( 3) SS BOND : angle 0.80105 ( 6) hydrogen bonds : bond 0.03831 ( 382) hydrogen bonds : angle 4.23900 ( 1075) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6283 (mpp) REVERT: B 226 VAL cc_start: 0.9451 (OUTLIER) cc_final: 0.9172 (m) REVERT: B 246 GLU cc_start: 0.8069 (tt0) cc_final: 0.7401 (mt-10) REVERT: C 52 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8067 (mtt-85) REVERT: C 220 GLN cc_start: 0.8023 (mt0) cc_final: 0.7761 (mt0) REVERT: E 82 GLN cc_start: 0.6145 (mm110) cc_final: 0.5765 (mp10) REVERT: E 156 SER cc_start: 0.8531 (t) cc_final: 0.8177 (m) outliers start: 21 outliers final: 15 residues processed: 142 average time/residue: 0.0838 time to fit residues: 17.3576 Evaluate side-chains 144 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107570 restraints weight = 24568.985| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.14 r_work: 0.3281 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 8632 Z= 0.148 Angle : 0.572 10.233 11750 Z= 0.305 Chirality : 0.043 0.186 1364 Planarity : 0.003 0.035 1483 Dihedral : 4.231 19.401 1205 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.31 % Allowed : 16.63 % Favored : 81.06 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1107 helix: 2.55 (0.28), residues: 356 sheet: -0.48 (0.34), residues: 253 loop : -0.98 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.026 0.001 TYR B 303 PHE 0.012 0.001 PHE C 335 TRP 0.010 0.001 TRP E 47 HIS 0.010 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8629) covalent geometry : angle 0.57164 (11744) SS BOND : bond 0.00539 ( 3) SS BOND : angle 0.87174 ( 6) hydrogen bonds : bond 0.03958 ( 382) hydrogen bonds : angle 4.30583 ( 1075) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 406 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6293 (mpp) REVERT: B 246 GLU cc_start: 0.8086 (tt0) cc_final: 0.7375 (mt-10) REVERT: C 52 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8080 (mtt-85) REVERT: C 220 GLN cc_start: 0.8031 (mt0) cc_final: 0.7756 (mt0) REVERT: E 82 GLN cc_start: 0.6209 (mm110) cc_final: 0.5819 (mp10) REVERT: E 156 SER cc_start: 0.8596 (t) cc_final: 0.8239 (m) outliers start: 20 outliers final: 16 residues processed: 138 average time/residue: 0.0805 time to fit residues: 16.0867 Evaluate side-chains 144 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 29 optimal weight: 0.0980 chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.138723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109001 restraints weight = 27924.380| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.15 r_work: 0.3351 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 8632 Z= 0.109 Angle : 0.534 10.054 11750 Z= 0.283 Chirality : 0.042 0.185 1364 Planarity : 0.003 0.033 1483 Dihedral : 3.959 17.623 1205 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.96 % Allowed : 17.44 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1107 helix: 2.65 (0.28), residues: 355 sheet: -0.39 (0.33), residues: 258 loop : -0.90 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.022 0.001 TYR B 303 PHE 0.008 0.001 PHE A 451 TRP 0.013 0.001 TRP C 82 HIS 0.007 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8629) covalent geometry : angle 0.53358 (11744) SS BOND : bond 0.00332 ( 3) SS BOND : angle 0.64953 ( 6) hydrogen bonds : bond 0.03429 ( 382) hydrogen bonds : angle 4.09871 ( 1075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2391.54 seconds wall clock time: 41 minutes 35.37 seconds (2495.37 seconds total)