Starting phenix.real_space_refine on Wed Feb 4 02:00:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9umx_64325/02_2026/9umx_64325.cif Found real_map, /net/cci-nas-00/data/ceres_data/9umx_64325/02_2026/9umx_64325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9umx_64325/02_2026/9umx_64325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9umx_64325/02_2026/9umx_64325.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9umx_64325/02_2026/9umx_64325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9umx_64325/02_2026/9umx_64325.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 47 5.16 5 C 5257 2.51 5 N 1414 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8217 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2208 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1497 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2432 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 382 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1613 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 68 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 2, 'TRANS': 5} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 1.71, per 1000 atoms: 0.21 Number of scatterers: 8217 At special positions: 0 Unit cell: (89.4956, 128.196, 131.825, 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 47 16.00 O 1499 8.00 N 1414 7.00 C 5257 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DAL D 9 " - " LEU D 8 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 298.8 milliseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 9 " Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 35.5% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 34 through 53 removed outlier: 3.581A pdb=" N ILE A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 removed outlier: 4.111A pdb=" N PHE A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.736A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.595A pdb=" N CYS A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 140 removed outlier: 3.697A pdb=" N SER A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 removed outlier: 3.510A pdb=" N CYS A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 199 through 230 removed outlier: 5.344A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 239 through 255 removed outlier: 3.798A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.839A pdb=" N GLN A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 303 removed outlier: 3.693A pdb=" N LEU A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASN A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.088A pdb=" N TYR A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 208 through 217 removed outlier: 4.212A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 216 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 217 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 330 through 351 removed outlier: 4.194A pdb=" N VAL B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 removed outlier: 3.618A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 37 removed outlier: 3.675A pdb=" N THR C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN C 35 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASN C 36 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.905A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.904A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.512A pdb=" N SER H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 removed outlier: 3.695A pdb=" N ARG A 178 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 190 " --> pdb=" O LYS D 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 191 removed outlier: 6.078A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 removed outlier: 6.078A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.655A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 63 removed outlier: 3.865A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS C 62 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP C 82 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 81 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.894A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.745A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.609A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.306A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 251 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.628A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.647A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 141 through 142 removed outlier: 3.571A pdb=" N ILE H 216 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 147 through 148 removed outlier: 3.509A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1077 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: 0.90 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2658 1.34 - 1.46: 2062 1.46 - 1.58: 3608 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 8389 Sorted by residual: bond pdb=" C VAL A 35 " pdb=" N PRO A 36 " ideal model delta sigma weight residual 1.334 1.364 -0.029 1.51e-02 4.39e+03 3.79e+00 bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.520 1.528 -0.008 8.80e-03 1.29e+04 8.81e-01 bond pdb=" CA GLU B 8 " pdb=" C GLU B 8 " ideal model delta sigma weight residual 1.518 1.553 -0.035 4.01e-02 6.22e+02 7.49e-01 bond pdb=" CB VAL C 71 " pdb=" CG2 VAL C 71 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.49e-01 bond pdb=" CB VAL H 97 " pdb=" CG2 VAL H 97 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.62e-01 ... (remaining 8384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 11350 2.52 - 5.03: 75 5.03 - 7.55: 8 7.55 - 10.07: 0 10.07 - 12.59: 2 Bond angle restraints: 11435 Sorted by residual: angle pdb=" N THR A 32 " pdb=" CA THR A 32 " pdb=" CB THR A 32 " ideal model delta sigma weight residual 111.50 100.83 10.67 1.70e+00 3.46e-01 3.94e+01 angle pdb=" C ARG A 34 " pdb=" N VAL A 35 " pdb=" CA VAL A 35 " ideal model delta sigma weight residual 120.24 123.79 -3.55 6.30e-01 2.52e+00 3.18e+01 angle pdb=" N THR A 32 " pdb=" CA THR A 32 " pdb=" C THR A 32 " ideal model delta sigma weight residual 111.00 98.41 12.59 2.80e+00 1.28e-01 2.02e+01 angle pdb=" C VAL A 35 " pdb=" CA VAL A 35 " pdb=" CB VAL A 35 " ideal model delta sigma weight residual 114.35 110.45 3.90 1.06e+00 8.90e-01 1.36e+01 angle pdb=" N THR A 235 " pdb=" CA THR A 235 " pdb=" C THR A 235 " ideal model delta sigma weight residual 114.56 110.06 4.50 1.27e+00 6.20e-01 1.25e+01 ... (remaining 11430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4496 17.76 - 35.53: 331 35.53 - 53.29: 55 53.29 - 71.05: 7 71.05 - 88.82: 5 Dihedral angle restraints: 4894 sinusoidal: 1641 harmonic: 3253 Sorted by residual: dihedral pdb=" N THR A 32 " pdb=" C THR A 32 " pdb=" CA THR A 32 " pdb=" CB THR A 32 " ideal model delta harmonic sigma weight residual 123.40 105.17 18.23 0 2.50e+00 1.60e-01 5.32e+01 dihedral pdb=" CA ALA C 56 " pdb=" C ALA C 56 " pdb=" N LYS C 57 " pdb=" CA LYS C 57 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 127.77 -34.77 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 4891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1320 0.109 - 0.218: 28 0.218 - 0.327: 0 0.327 - 0.437: 0 0.437 - 0.546: 1 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA THR A 32 " pdb=" N THR A 32 " pdb=" C THR A 32 " pdb=" CB THR A 32 " both_signs ideal model delta sigma weight residual False 2.53 3.07 -0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE H 189 " pdb=" N ILE H 189 " pdb=" C ILE H 189 " pdb=" CB ILE H 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 1346 not shown) Planarity restraints: 1451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO C 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO G 49 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 35 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 36 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.019 5.00e-02 4.00e+02 ... (remaining 1448 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1032 2.75 - 3.29: 7388 3.29 - 3.83: 12408 3.83 - 4.36: 13318 4.36 - 4.90: 25032 Nonbonded interactions: 59178 Sorted by model distance: nonbonded pdb=" O LYS B 35 " pdb=" OG1 THR B 220 " model vdw 2.218 3.040 nonbonded pdb=" OG SER B 314 " pdb=" OD1 ASN B 316 " model vdw 2.250 3.040 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP G 48 " model vdw 2.277 3.040 nonbonded pdb=" NH1 ARG B 15 " pdb=" O VAL C 90 " model vdw 2.301 3.120 nonbonded pdb=" OD1 ASP C 163 " pdb=" OG1 THR C 165 " model vdw 2.383 3.040 ... (remaining 59173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.570 Find NCS groups from input model: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.002 0.035 8393 Z= 0.116 Angle : 0.549 12.586 11444 Z= 0.297 Chirality : 0.043 0.546 1349 Planarity : 0.004 0.043 1450 Dihedral : 13.032 88.817 2782 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.26), residues: 1106 helix: 1.87 (0.28), residues: 373 sheet: -0.11 (0.32), residues: 271 loop : -1.87 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 10 TYR 0.010 0.001 TYR B 354 PHE 0.011 0.001 PHE C 199 TRP 0.018 0.001 TRP C 211 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8389) covalent geometry : angle 0.54851 (11435) SS BOND : bond 0.00450 ( 3) SS BOND : angle 0.89587 ( 6) hydrogen bonds : bond 0.19314 ( 379) hydrogen bonds : angle 6.24928 ( 1077) link_TRANS : bond 0.00245 ( 1) link_TRANS : angle 0.71976 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 86 CYS cc_start: 0.7110 (t) cc_final: 0.6891 (t) REVERT: A 209 LEU cc_start: 0.8062 (tp) cc_final: 0.7849 (tt) REVERT: A 228 ARG cc_start: 0.6708 (tpp80) cc_final: 0.5798 (tpp80) REVERT: B 14 GLU cc_start: 0.7325 (tt0) cc_final: 0.7104 (tt0) REVERT: B 44 SER cc_start: 0.7953 (m) cc_final: 0.7643 (m) REVERT: B 189 HIS cc_start: 0.8051 (p90) cc_final: 0.7582 (p90) REVERT: C 22 ARG cc_start: 0.7564 (ttm170) cc_final: 0.7254 (mtm-85) REVERT: C 29 THR cc_start: 0.8433 (t) cc_final: 0.8155 (p) REVERT: C 49 ARG cc_start: 0.8456 (mmt-90) cc_final: 0.7893 (mpt180) REVERT: C 61 MET cc_start: 0.7625 (ppp) cc_final: 0.7219 (ppp) REVERT: C 247 ASP cc_start: 0.7172 (t0) cc_final: 0.6894 (t0) REVERT: C 280 LYS cc_start: 0.8860 (tptp) cc_final: 0.8596 (tttp) REVERT: C 304 ARG cc_start: 0.6046 (mmp-170) cc_final: 0.4389 (ttm170) REVERT: C 322 ASP cc_start: 0.7663 (m-30) cc_final: 0.7448 (m-30) REVERT: H 12 VAL cc_start: 0.8637 (t) cc_final: 0.8302 (p) REVERT: D 6 MET cc_start: 0.7171 (mmt) cc_final: 0.6970 (mmm) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0987 time to fit residues: 26.3900 Evaluate side-chains 159 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 194 ASN B 346 ASN C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101207 restraints weight = 12979.115| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.27 r_work: 0.3163 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8393 Z= 0.149 Angle : 0.572 6.359 11444 Z= 0.305 Chirality : 0.042 0.134 1349 Planarity : 0.004 0.038 1450 Dihedral : 4.057 23.213 1199 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.65 % Allowed : 10.47 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.26), residues: 1106 helix: 1.75 (0.28), residues: 375 sheet: 0.22 (0.32), residues: 272 loop : -1.98 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 134 TYR 0.021 0.002 TYR H 59 PHE 0.015 0.001 PHE C 241 TRP 0.009 0.001 TRP C 82 HIS 0.004 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8389) covalent geometry : angle 0.57181 (11435) SS BOND : bond 0.00878 ( 3) SS BOND : angle 1.26106 ( 6) hydrogen bonds : bond 0.05318 ( 379) hydrogen bonds : angle 4.45525 ( 1077) link_TRANS : bond 0.00038 ( 1) link_TRANS : angle 0.61441 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.299 Fit side-chains REVERT: A 86 CYS cc_start: 0.7872 (t) cc_final: 0.7549 (t) REVERT: A 178 ARG cc_start: 0.7665 (mtp-110) cc_final: 0.7336 (mtp180) REVERT: A 228 ARG cc_start: 0.7151 (tpp80) cc_final: 0.6238 (tpp80) REVERT: B 14 GLU cc_start: 0.7852 (tt0) cc_final: 0.7651 (tt0) REVERT: B 44 SER cc_start: 0.8119 (m) cc_final: 0.7773 (m) REVERT: B 189 HIS cc_start: 0.8402 (p90) cc_final: 0.7899 (p-80) REVERT: B 297 TYR cc_start: 0.7543 (t80) cc_final: 0.7149 (t80) REVERT: B 346 ASN cc_start: 0.8171 (m-40) cc_final: 0.7740 (m110) REVERT: C 61 MET cc_start: 0.8260 (ppp) cc_final: 0.7787 (ppp) REVERT: C 227 SER cc_start: 0.7899 (t) cc_final: 0.7696 (m) REVERT: C 233 CYS cc_start: 0.8285 (p) cc_final: 0.8031 (t) REVERT: C 247 ASP cc_start: 0.7796 (t0) cc_final: 0.7385 (t0) REVERT: C 280 LYS cc_start: 0.9159 (tptp) cc_final: 0.8881 (tttp) REVERT: C 304 ARG cc_start: 0.6612 (mmp-170) cc_final: 0.3613 (ttm110) REVERT: H 12 VAL cc_start: 0.8022 (t) cc_final: 0.7644 (p) REVERT: H 178 LEU cc_start: 0.8713 (tt) cc_final: 0.8464 (tp) REVERT: D 6 MET cc_start: 0.8035 (mmt) cc_final: 0.7738 (mmm) outliers start: 21 outliers final: 17 residues processed: 179 average time/residue: 0.1055 time to fit residues: 24.3955 Evaluate side-chains 181 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 106 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN B 347 ASN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100199 restraints weight = 12916.202| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.27 r_work: 0.3148 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8393 Z= 0.149 Angle : 0.565 6.248 11444 Z= 0.302 Chirality : 0.042 0.141 1349 Planarity : 0.004 0.036 1450 Dihedral : 4.102 24.662 1199 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.53 % Allowed : 14.75 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.25), residues: 1106 helix: 1.71 (0.28), residues: 375 sheet: 0.40 (0.32), residues: 266 loop : -1.98 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 134 TYR 0.019 0.002 TYR C 105 PHE 0.014 0.001 PHE C 241 TRP 0.011 0.001 TRP A 74 HIS 0.004 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8389) covalent geometry : angle 0.56425 (11435) SS BOND : bond 0.00903 ( 3) SS BOND : angle 1.17754 ( 6) hydrogen bonds : bond 0.05365 ( 379) hydrogen bonds : angle 4.28888 ( 1077) link_TRANS : bond 0.00020 ( 1) link_TRANS : angle 0.63555 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.214 Fit side-chains REVERT: A 178 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.7584 (mtp180) REVERT: A 198 ARG cc_start: 0.8222 (tmm-80) cc_final: 0.7926 (ttm-80) REVERT: A 228 ARG cc_start: 0.7209 (tpp80) cc_final: 0.6244 (tpp80) REVERT: B 14 GLU cc_start: 0.7760 (tt0) cc_final: 0.7555 (tt0) REVERT: B 44 SER cc_start: 0.8202 (m) cc_final: 0.7829 (m) REVERT: B 189 HIS cc_start: 0.8341 (p90) cc_final: 0.7844 (p-80) REVERT: C 61 MET cc_start: 0.8348 (ppp) cc_final: 0.7848 (ppp) REVERT: C 227 SER cc_start: 0.8095 (t) cc_final: 0.7883 (m) REVERT: C 247 ASP cc_start: 0.7751 (t0) cc_final: 0.7165 (t0) REVERT: C 304 ARG cc_start: 0.6807 (mmp-170) cc_final: 0.4804 (mmt-90) REVERT: H 12 VAL cc_start: 0.8133 (t) cc_final: 0.7758 (p) REVERT: D 6 MET cc_start: 0.8005 (mmt) cc_final: 0.7575 (mmm) outliers start: 28 outliers final: 20 residues processed: 183 average time/residue: 0.0874 time to fit residues: 20.8302 Evaluate side-chains 183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 64 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 346 ASN B 347 ASN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.117690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099330 restraints weight = 13144.093| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.29 r_work: 0.3133 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8393 Z= 0.152 Angle : 0.563 6.320 11444 Z= 0.300 Chirality : 0.042 0.140 1349 Planarity : 0.004 0.037 1450 Dihedral : 4.179 24.893 1199 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.04 % Allowed : 15.89 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1106 helix: 1.79 (0.28), residues: 370 sheet: 0.46 (0.33), residues: 264 loop : -2.02 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 134 TYR 0.016 0.002 TYR H 59 PHE 0.014 0.001 PHE C 241 TRP 0.013 0.001 TRP A 74 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8389) covalent geometry : angle 0.56209 (11435) SS BOND : bond 0.00919 ( 3) SS BOND : angle 1.32495 ( 6) hydrogen bonds : bond 0.05389 ( 379) hydrogen bonds : angle 4.21944 ( 1077) link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 0.64959 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.202 Fit side-chains REVERT: A 198 ARG cc_start: 0.8207 (tmm-80) cc_final: 0.7915 (ttm-80) REVERT: A 228 ARG cc_start: 0.7186 (tpp80) cc_final: 0.6221 (tpp80) REVERT: B 44 SER cc_start: 0.8140 (m) cc_final: 0.7761 (m) REVERT: B 189 HIS cc_start: 0.8204 (p90) cc_final: 0.7795 (p-80) REVERT: B 346 ASN cc_start: 0.8224 (m-40) cc_final: 0.7739 (m-40) REVERT: C 61 MET cc_start: 0.8379 (ppp) cc_final: 0.7908 (ppp) REVERT: C 247 ASP cc_start: 0.7746 (t0) cc_final: 0.7143 (t0) REVERT: C 273 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8191 (mt) REVERT: C 304 ARG cc_start: 0.6868 (mmp-170) cc_final: 0.4786 (mmt-90) REVERT: H 12 VAL cc_start: 0.8143 (t) cc_final: 0.7746 (p) REVERT: H 71 SER cc_start: 0.8418 (m) cc_final: 0.7888 (p) REVERT: H 87 ARG cc_start: 0.7722 (mtt-85) cc_final: 0.7502 (mtt90) REVERT: D 6 MET cc_start: 0.8012 (mmt) cc_final: 0.7573 (mmm) outliers start: 32 outliers final: 24 residues processed: 189 average time/residue: 0.0908 time to fit residues: 22.1727 Evaluate side-chains 186 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 TYR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 0.0060 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 10 optimal weight: 0.0980 chunk 26 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 0.0040 overall best weight: 0.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 259 GLN H 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106277 restraints weight = 13021.671| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.15 r_work: 0.3261 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8393 Z= 0.091 Angle : 0.482 5.506 11444 Z= 0.253 Chirality : 0.039 0.146 1349 Planarity : 0.003 0.038 1450 Dihedral : 3.599 23.168 1199 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.02 % Allowed : 19.80 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1106 helix: 1.95 (0.27), residues: 369 sheet: 0.49 (0.33), residues: 266 loop : -1.83 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 134 TYR 0.012 0.001 TYR H 190 PHE 0.011 0.001 PHE A 93 TRP 0.010 0.001 TRP A 255 HIS 0.004 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 8389) covalent geometry : angle 0.48158 (11435) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.80463 ( 6) hydrogen bonds : bond 0.02910 ( 379) hydrogen bonds : angle 3.72180 ( 1077) link_TRANS : bond 0.00219 ( 1) link_TRANS : angle 0.75756 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.256 Fit side-chains REVERT: A 178 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7416 (ttp-170) REVERT: A 198 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7768 (ttm-80) REVERT: A 228 ARG cc_start: 0.7025 (tpp80) cc_final: 0.6168 (tpp80) REVERT: B 44 SER cc_start: 0.8145 (m) cc_final: 0.7802 (m) REVERT: B 253 SER cc_start: 0.8892 (t) cc_final: 0.8437 (p) REVERT: B 346 ASN cc_start: 0.7919 (m-40) cc_final: 0.7473 (m-40) REVERT: C 29 THR cc_start: 0.8194 (t) cc_final: 0.7763 (p) REVERT: C 61 MET cc_start: 0.8308 (ppp) cc_final: 0.7895 (ppp) REVERT: C 70 LEU cc_start: 0.8403 (mt) cc_final: 0.7938 (tp) REVERT: C 71 VAL cc_start: 0.7455 (t) cc_final: 0.6799 (p) REVERT: C 129 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7704 (ttt-90) REVERT: C 156 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: C 247 ASP cc_start: 0.7653 (t0) cc_final: 0.7001 (t0) REVERT: C 304 ARG cc_start: 0.6535 (mmp-170) cc_final: 0.3788 (ttm170) REVERT: H 12 VAL cc_start: 0.8032 (t) cc_final: 0.7631 (p) REVERT: H 59 TYR cc_start: 0.8174 (m-80) cc_final: 0.7654 (m-80) REVERT: H 60 TYR cc_start: 0.8853 (m-80) cc_final: 0.8416 (m-80) REVERT: H 71 SER cc_start: 0.8374 (m) cc_final: 0.7783 (p) REVERT: D 6 MET cc_start: 0.7950 (mmt) cc_final: 0.7494 (mmm) outliers start: 16 outliers final: 11 residues processed: 186 average time/residue: 0.0974 time to fit residues: 23.6131 Evaluate side-chains 178 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.098906 restraints weight = 12895.248| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.24 r_work: 0.3139 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8393 Z= 0.160 Angle : 0.560 6.310 11444 Z= 0.300 Chirality : 0.042 0.177 1349 Planarity : 0.004 0.038 1450 Dihedral : 4.006 23.888 1199 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.66 % Allowed : 19.80 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1106 helix: 1.90 (0.28), residues: 371 sheet: 0.40 (0.32), residues: 271 loop : -1.90 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 134 TYR 0.015 0.002 TYR H 59 PHE 0.031 0.002 PHE B 275 TRP 0.012 0.001 TRP A 74 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8389) covalent geometry : angle 0.55992 (11435) SS BOND : bond 0.00946 ( 3) SS BOND : angle 1.22908 ( 6) hydrogen bonds : bond 0.05275 ( 379) hydrogen bonds : angle 4.02777 ( 1077) link_TRANS : bond 0.00035 ( 1) link_TRANS : angle 0.62491 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.197 Fit side-chains REVERT: A 198 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7886 (ttm-80) REVERT: B 44 SER cc_start: 0.8088 (m) cc_final: 0.7761 (m) REVERT: C 59 TYR cc_start: 0.8351 (m-80) cc_final: 0.8079 (m-80) REVERT: C 61 MET cc_start: 0.8338 (ppp) cc_final: 0.7925 (ppp) REVERT: C 75 GLN cc_start: 0.8158 (tp40) cc_final: 0.7944 (mm110) REVERT: C 161 SER cc_start: 0.8324 (m) cc_final: 0.8046 (p) REVERT: C 247 ASP cc_start: 0.7676 (t0) cc_final: 0.7064 (t0) REVERT: C 270 ILE cc_start: 0.8906 (pt) cc_final: 0.8483 (mm) REVERT: C 304 ARG cc_start: 0.6774 (mmp-170) cc_final: 0.3892 (ttm170) REVERT: H 12 VAL cc_start: 0.8120 (t) cc_final: 0.7743 (p) REVERT: H 60 TYR cc_start: 0.8966 (m-80) cc_final: 0.8549 (m-80) REVERT: H 71 SER cc_start: 0.8352 (m) cc_final: 0.7843 (p) REVERT: H 80 PHE cc_start: 0.7983 (m-80) cc_final: 0.7603 (m-80) REVERT: D 6 MET cc_start: 0.7988 (mmt) cc_final: 0.7565 (mmm) outliers start: 29 outliers final: 28 residues processed: 177 average time/residue: 0.0944 time to fit residues: 21.6939 Evaluate side-chains 183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 0.3980 chunk 11 optimal weight: 0.0670 chunk 56 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN B 346 ASN B 347 ASN C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100581 restraints weight = 13022.964| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.15 r_work: 0.3174 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8393 Z= 0.119 Angle : 0.537 6.576 11444 Z= 0.284 Chirality : 0.041 0.188 1349 Planarity : 0.004 0.039 1450 Dihedral : 3.972 25.119 1199 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.03 % Allowed : 21.82 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1106 helix: 1.90 (0.28), residues: 371 sheet: 0.32 (0.32), residues: 278 loop : -1.77 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 134 TYR 0.011 0.001 TYR H 190 PHE 0.015 0.001 PHE B 275 TRP 0.012 0.001 TRP A 74 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8389) covalent geometry : angle 0.53628 (11435) SS BOND : bond 0.00705 ( 3) SS BOND : angle 1.10592 ( 6) hydrogen bonds : bond 0.04496 ( 379) hydrogen bonds : angle 3.92776 ( 1077) link_TRANS : bond 0.00087 ( 1) link_TRANS : angle 0.69083 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.263 Fit side-chains REVERT: A 198 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: B 44 SER cc_start: 0.8126 (m) cc_final: 0.7726 (m) REVERT: C 29 THR cc_start: 0.8155 (t) cc_final: 0.7753 (p) REVERT: C 61 MET cc_start: 0.8325 (ppp) cc_final: 0.7898 (ppp) REVERT: C 161 SER cc_start: 0.8128 (m) cc_final: 0.7892 (p) REVERT: C 247 ASP cc_start: 0.7619 (t0) cc_final: 0.7016 (t0) REVERT: C 270 ILE cc_start: 0.8886 (pt) cc_final: 0.8469 (mm) REVERT: C 304 ARG cc_start: 0.6694 (mmp-170) cc_final: 0.3854 (ttm170) REVERT: H 12 VAL cc_start: 0.8103 (t) cc_final: 0.7703 (p) REVERT: H 60 TYR cc_start: 0.8943 (m-80) cc_final: 0.8529 (m-80) REVERT: H 71 SER cc_start: 0.8386 (m) cc_final: 0.7847 (p) REVERT: H 80 PHE cc_start: 0.7932 (m-80) cc_final: 0.7557 (m-80) REVERT: D 6 MET cc_start: 0.7951 (mmt) cc_final: 0.7515 (mmm) outliers start: 24 outliers final: 22 residues processed: 173 average time/residue: 0.0883 time to fit residues: 19.7635 Evaluate side-chains 178 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 0.0070 chunk 28 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 346 ASN B 347 ASN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098562 restraints weight = 13067.375| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.28 r_work: 0.3136 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8393 Z= 0.149 Angle : 0.565 6.331 11444 Z= 0.301 Chirality : 0.042 0.185 1349 Planarity : 0.004 0.039 1450 Dihedral : 4.104 25.052 1199 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.41 % Allowed : 20.18 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1106 helix: 1.82 (0.28), residues: 372 sheet: 0.31 (0.32), residues: 277 loop : -1.88 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 134 TYR 0.014 0.001 TYR H 59 PHE 0.023 0.001 PHE B 275 TRP 0.013 0.001 TRP A 74 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8389) covalent geometry : angle 0.56396 (11435) SS BOND : bond 0.00887 ( 3) SS BOND : angle 1.28338 ( 6) hydrogen bonds : bond 0.05243 ( 379) hydrogen bonds : angle 4.07417 ( 1077) link_TRANS : bond 0.00006 ( 1) link_TRANS : angle 0.65744 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.179 Fit side-chains REVERT: A 198 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7776 (ttm-80) REVERT: B 44 SER cc_start: 0.8209 (m) cc_final: 0.7848 (m) REVERT: C 29 THR cc_start: 0.8186 (t) cc_final: 0.7834 (p) REVERT: C 61 MET cc_start: 0.8360 (ppp) cc_final: 0.7947 (ppp) REVERT: C 161 SER cc_start: 0.8318 (m) cc_final: 0.8091 (p) REVERT: C 211 TRP cc_start: 0.8056 (OUTLIER) cc_final: 0.6385 (m-10) REVERT: C 247 ASP cc_start: 0.7669 (t0) cc_final: 0.7092 (t0) REVERT: C 270 ILE cc_start: 0.8892 (pt) cc_final: 0.8488 (mm) REVERT: C 304 ARG cc_start: 0.6898 (mmp-170) cc_final: 0.4806 (mmt-90) REVERT: H 12 VAL cc_start: 0.8110 (t) cc_final: 0.7735 (p) REVERT: H 60 TYR cc_start: 0.8963 (m-80) cc_final: 0.8548 (m-80) REVERT: H 71 SER cc_start: 0.8399 (m) cc_final: 0.7880 (p) REVERT: H 80 PHE cc_start: 0.7978 (m-80) cc_final: 0.7607 (m-80) REVERT: D 6 MET cc_start: 0.7999 (mmt) cc_final: 0.7558 (mmm) outliers start: 35 outliers final: 32 residues processed: 188 average time/residue: 0.0891 time to fit residues: 21.8045 Evaluate side-chains 192 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 ASN B 346 ASN B 347 ASN C 75 GLN C 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099782 restraints weight = 12947.048| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.14 r_work: 0.3151 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8393 Z= 0.139 Angle : 0.560 6.828 11444 Z= 0.297 Chirality : 0.042 0.173 1349 Planarity : 0.004 0.042 1450 Dihedral : 4.094 25.313 1199 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.41 % Allowed : 20.43 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.26), residues: 1106 helix: 1.85 (0.28), residues: 370 sheet: 0.30 (0.32), residues: 278 loop : -1.91 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 134 TYR 0.012 0.001 TYR H 59 PHE 0.018 0.001 PHE A 93 TRP 0.013 0.001 TRP A 74 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8389) covalent geometry : angle 0.55886 (11435) SS BOND : bond 0.00823 ( 3) SS BOND : angle 1.27184 ( 6) hydrogen bonds : bond 0.04976 ( 379) hydrogen bonds : angle 4.03123 ( 1077) link_TRANS : bond 0.00014 ( 1) link_TRANS : angle 0.68340 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.201 Fit side-chains REVERT: A 198 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7731 (ttm-80) REVERT: B 44 SER cc_start: 0.8146 (m) cc_final: 0.7758 (m) REVERT: C 29 THR cc_start: 0.8143 (t) cc_final: 0.7737 (p) REVERT: C 61 MET cc_start: 0.8346 (ppp) cc_final: 0.7923 (ppp) REVERT: C 161 SER cc_start: 0.8302 (m) cc_final: 0.8042 (p) REVERT: C 211 TRP cc_start: 0.8033 (OUTLIER) cc_final: 0.6358 (m-10) REVERT: C 247 ASP cc_start: 0.7629 (t0) cc_final: 0.7050 (t0) REVERT: C 270 ILE cc_start: 0.8877 (pt) cc_final: 0.8478 (mm) REVERT: C 304 ARG cc_start: 0.6773 (mmp-170) cc_final: 0.4740 (mmt-90) REVERT: H 12 VAL cc_start: 0.8126 (t) cc_final: 0.7727 (p) REVERT: H 60 TYR cc_start: 0.8954 (m-80) cc_final: 0.8536 (m-80) REVERT: H 71 SER cc_start: 0.8376 (m) cc_final: 0.7831 (p) REVERT: H 80 PHE cc_start: 0.7945 (m-80) cc_final: 0.7571 (m-80) REVERT: D 6 MET cc_start: 0.7960 (mmt) cc_final: 0.7505 (mmm) outliers start: 35 outliers final: 32 residues processed: 186 average time/residue: 0.0940 time to fit residues: 22.6353 Evaluate side-chains 194 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.0030 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 chunk 45 optimal weight: 0.0970 chunk 92 optimal weight: 0.6980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 346 ASN B 347 ASN C 75 GLN C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102956 restraints weight = 12903.726| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.18 r_work: 0.3198 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8393 Z= 0.101 Angle : 0.514 5.917 11444 Z= 0.271 Chirality : 0.040 0.154 1349 Planarity : 0.004 0.047 1450 Dihedral : 3.783 23.433 1199 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.03 % Allowed : 21.82 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1106 helix: 2.00 (0.28), residues: 369 sheet: 0.33 (0.33), residues: 270 loop : -1.79 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 134 TYR 0.013 0.001 TYR H 190 PHE 0.019 0.001 PHE A 93 TRP 0.010 0.001 TRP A 74 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8389) covalent geometry : angle 0.51329 (11435) SS BOND : bond 0.00468 ( 3) SS BOND : angle 0.98662 ( 6) hydrogen bonds : bond 0.03670 ( 379) hydrogen bonds : angle 3.78959 ( 1077) link_TRANS : bond 0.00144 ( 1) link_TRANS : angle 0.73338 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.277 Fit side-chains REVERT: A 198 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7690 (ttm-80) REVERT: A 228 ARG cc_start: 0.7054 (tpp80) cc_final: 0.6078 (tpp80) REVERT: B 44 SER cc_start: 0.8151 (m) cc_final: 0.7790 (m) REVERT: B 253 SER cc_start: 0.8903 (t) cc_final: 0.8459 (p) REVERT: B 346 ASN cc_start: 0.8064 (m-40) cc_final: 0.7649 (m-40) REVERT: C 61 MET cc_start: 0.8322 (ppp) cc_final: 0.7945 (ppp) REVERT: C 70 LEU cc_start: 0.8470 (mt) cc_final: 0.7964 (tp) REVERT: C 71 VAL cc_start: 0.7628 (OUTLIER) cc_final: 0.6986 (p) REVERT: C 161 SER cc_start: 0.8204 (m) cc_final: 0.7908 (p) REVERT: C 247 ASP cc_start: 0.7608 (t0) cc_final: 0.7000 (t0) REVERT: C 270 ILE cc_start: 0.8870 (pt) cc_final: 0.8469 (mm) REVERT: C 304 ARG cc_start: 0.6690 (mmp-170) cc_final: 0.3826 (ttm170) REVERT: H 12 VAL cc_start: 0.8024 (t) cc_final: 0.7633 (p) REVERT: H 60 TYR cc_start: 0.8888 (m-80) cc_final: 0.8494 (m-80) REVERT: H 71 SER cc_start: 0.8387 (m) cc_final: 0.7819 (p) REVERT: H 226 VAL cc_start: 0.8115 (t) cc_final: 0.7830 (t) REVERT: D 6 MET cc_start: 0.7958 (mmt) cc_final: 0.7522 (mmm) outliers start: 24 outliers final: 21 residues processed: 177 average time/residue: 0.1191 time to fit residues: 27.0347 Evaluate side-chains 177 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 290 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098537 restraints weight = 12931.411| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.26 r_work: 0.3134 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8393 Z= 0.158 Angle : 0.568 6.543 11444 Z= 0.304 Chirality : 0.043 0.165 1349 Planarity : 0.004 0.044 1450 Dihedral : 4.087 24.859 1199 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.66 % Allowed : 22.07 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1106 helix: 1.86 (0.28), residues: 372 sheet: 0.33 (0.33), residues: 273 loop : -1.86 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 134 TYR 0.015 0.001 TYR H 59 PHE 0.031 0.001 PHE A 93 TRP 0.013 0.001 TRP A 74 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8389) covalent geometry : angle 0.56766 (11435) SS BOND : bond 0.00910 ( 3) SS BOND : angle 1.28732 ( 6) hydrogen bonds : bond 0.05295 ( 379) hydrogen bonds : angle 4.05919 ( 1077) link_TRANS : bond 0.00022 ( 1) link_TRANS : angle 0.64339 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1935.77 seconds wall clock time: 33 minutes 41.62 seconds (2021.62 seconds total)