Starting phenix.real_space_refine on Wed Sep 17 14:45:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hd0_34668/09_2025/8hd0_34668.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hd0_34668/09_2025/8hd0_34668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hd0_34668/09_2025/8hd0_34668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hd0_34668/09_2025/8hd0_34668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hd0_34668/09_2025/8hd0_34668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hd0_34668/09_2025/8hd0_34668.map" } resolution = 3.11 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 5699 2.51 5 N 1682 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9096 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 210} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 210} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1918 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 11, 'ARG:plan': 8, 'ASP:plan': 14, 'GLN:plan1': 10, 'TYR:plan': 4, 'PHE:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 248 Chain: "D" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1888 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 337 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ASN:plan1': 6, 'GLU:plan': 11, 'GLN:plan1': 13, 'ARG:plan': 9, 'TYR:plan': 3, 'ASP:plan': 12, 'PHE:plan': 5, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 264 Chain: "E" Number of atoms: 1889 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 1869 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 8, 'TRANS': 371} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1137 Unresolved non-hydrogen angles: 1428 Unresolved non-hydrogen dihedrals: 923 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 49, 'ASP:plan': 7, 'GLU:plan': 36, 'ARG:plan': 34, 'ASN:plan1': 10, 'PHE:plan': 4, 'HIS:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 704 Conformer: "B" Number of residues, atoms: 380, 1869 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 300} Link IDs: {'PTRANS': 8, 'TRANS': 371} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1137 Unresolved non-hydrogen angles: 1428 Unresolved non-hydrogen dihedrals: 923 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 49, 'ASP:plan': 7, 'GLU:plan': 36, 'ARG:plan': 34, 'ASN:plan1': 10, 'PHE:plan': 4, 'HIS:plan': 3, 'TYR:plan': 9, 'TRP:plan': 4, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 704 bond proxies already assigned to first conformer: 1844 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLU E 233 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLU E 233 " occ=0.50 residue: pdb=" N AARG E 237 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG E 237 " occ=0.50 residue: pdb=" N AARG E 262 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG E 262 " occ=0.50 residue: pdb=" N AVAL E 302 " occ=0.50 ... (8 atoms not shown) pdb=" CB BVAL E 302 " occ=0.50 Time building chain proxies: 2.42, per 1000 atoms: 0.27 Number of scatterers: 9096 At special positions: 0 Unit cell: (68.04, 91.56, 253.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 6 15.00 O 1679 8.00 N 1682 7.00 C 5699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 502.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 58.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.608A pdb=" N LEU A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 108 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.857A pdb=" N VAL A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 169 through 185 Processing helix chain 'A' and resid 196 through 201 removed outlier: 4.217A pdb=" N ILE A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 95 through 108 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 110 through 124 Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.505A pdb=" N ALA B 131 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.604A pdb=" N LEU B 138 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 169 through 185 Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.586A pdb=" N ARG B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 79 Processing helix chain 'C' and resid 80 through 107 removed outlier: 3.635A pdb=" N VAL C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Proline residue: C 98 - end of helix removed outlier: 4.186A pdb=" N MET C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 105 " --> pdb=" O CYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.887A pdb=" N ALA C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 165 removed outlier: 3.856A pdb=" N GLY C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 3.609A pdb=" N GLY C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 207 removed outlier: 3.632A pdb=" N THR C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 229 through 261 removed outlier: 3.680A pdb=" N SER C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.668A pdb=" N ILE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 300 removed outlier: 3.511A pdb=" N GLY C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 320 removed outlier: 3.925A pdb=" N SER C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 355 removed outlier: 4.134A pdb=" N LEU C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 79 Processing helix chain 'D' and resid 80 through 116 removed outlier: 4.159A pdb=" N LEU D 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Proline residue: D 98 - end of helix removed outlier: 3.641A pdb=" N TYR D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 141 Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.573A pdb=" N GLY D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE D 162 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 3.912A pdb=" N GLY D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 removed outlier: 5.036A pdb=" N THR D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 261 removed outlier: 4.306A pdb=" N SER D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 271 removed outlier: 4.333A pdb=" N GLN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 319 removed outlier: 3.512A pdb=" N ARG D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) Proline residue: D 281 - end of helix removed outlier: 3.789A pdb=" N LEU D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL D 312 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 359 removed outlier: 3.548A pdb=" N ARG D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS D 358 " --> pdb=" O GLN D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 51 Processing helix chain 'E' and resid 52 through 123 removed outlier: 4.657A pdb=" N GLN E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 152 through 217 Processing helix chain 'E' and resid 221 through 247 Processing helix chain 'E' and resid 248 through 271 removed outlier: 4.129A pdb=" N GLU E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 286 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 25 removed outlier: 5.436A pdb=" N GLN A 19 " --> pdb=" O LYS A 9 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS A 9 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N PHE A 23 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU A 5 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N MET A 25 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG A 3 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL A 7 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 56 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 6.465A pdb=" N LEU A 159 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA A 193 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 161 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 31 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 32 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU A 210 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR A 34 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 25 removed outlier: 6.492A pdb=" N ALA B 17 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA B 10 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN B 19 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER B 8 " --> pdb=" O GLN B 19 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 21 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL B 7 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA B 56 " --> pdb=" O VAL B 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 84 removed outlier: 6.401A pdb=" N GLY B 82 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP B 162 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 84 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 159 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA B 193 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 161 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 31 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AA7, first strand: chain 'E' and resid 313 through 315 removed outlier: 4.487A pdb=" N GLN E 315 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU E 318 " --> pdb=" O GLN E 315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 322 through 326 removed outlier: 4.408A pdb=" N ILE E 404 " --> pdb=" O VAL E 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 340 through 344 removed outlier: 4.711A pdb=" N VAL E 341 " --> pdb=" O GLU E 357 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU E 357 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 354 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL E 356 " --> pdb=" O SER E 364 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER E 364 " --> pdb=" O VAL E 356 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2854 1.33 - 1.45: 1165 1.45 - 1.57: 5142 1.57 - 1.69: 10 1.69 - 1.81: 52 Bond restraints: 9223 Sorted by residual: bond pdb=" N VAL C 185 " pdb=" CA VAL C 185 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.19e-02 7.06e+03 9.58e+00 bond pdb=" N VAL C 186 " pdb=" CA VAL C 186 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 9.06e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.72e+00 bond pdb=" N ILE C 121 " pdb=" CA ILE C 121 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.02e+00 bond pdb=" N ILE C 211 " pdb=" CA ILE C 211 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.96e+00 ... (remaining 9218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 12395 2.48 - 4.95: 214 4.95 - 7.43: 23 7.43 - 9.90: 3 9.90 - 12.38: 2 Bond angle restraints: 12637 Sorted by residual: angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 129.08 10.79 1.00e+00 1.00e+00 1.16e+02 angle pdb=" PB ATP A 301 " pdb=" O3B ATP A 301 " pdb=" PG ATP A 301 " ideal model delta sigma weight residual 139.87 130.49 9.38 1.00e+00 1.00e+00 8.80e+01 angle pdb=" N ALA C 225 " pdb=" CA ALA C 225 " pdb=" C ALA C 225 " ideal model delta sigma weight residual 114.62 108.03 6.59 1.14e+00 7.69e-01 3.34e+01 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 131.79 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N VAL C 100 " pdb=" CA VAL C 100 " pdb=" C VAL C 100 " ideal model delta sigma weight residual 112.96 108.55 4.41 1.00e+00 1.00e+00 1.95e+01 ... (remaining 12632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4856 16.99 - 33.98: 379 33.98 - 50.97: 158 50.97 - 67.95: 37 67.95 - 84.94: 8 Dihedral angle restraints: 5438 sinusoidal: 1414 harmonic: 4024 Sorted by residual: dihedral pdb=" CA GLU E 114 " pdb=" C GLU E 114 " pdb=" N ARG E 115 " pdb=" CA ARG E 115 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA HIS A 195 " pdb=" C HIS A 195 " pdb=" N ASP A 196 " pdb=" CA ASP A 196 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA SER D 264 " pdb=" C SER D 264 " pdb=" N ILE D 265 " pdb=" CA ILE D 265 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 5435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1355 0.066 - 0.131: 173 0.131 - 0.197: 28 0.197 - 0.262: 4 0.262 - 0.328: 2 Chirality restraints: 1562 Sorted by residual: chirality pdb=" CB THR C 360 " pdb=" CA THR C 360 " pdb=" OG1 THR C 360 " pdb=" CG2 THR C 360 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB VAL B 96 " pdb=" CA VAL B 96 " pdb=" CG1 VAL B 96 " pdb=" CG2 VAL B 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA LEU C 198 " pdb=" N LEU C 198 " pdb=" C LEU C 198 " pdb=" CB LEU C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1559 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 110 " 0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C LYS E 110 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS E 110 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA E 111 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 280 " 0.060 5.00e-02 4.00e+02 9.00e-02 1.29e+01 pdb=" N PRO D 281 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 104 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ALA E 104 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA E 104 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS E 105 " -0.017 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 104 2.64 - 3.21: 8615 3.21 - 3.77: 13968 3.77 - 4.34: 17617 4.34 - 4.90: 29660 Nonbonded interactions: 69964 Sorted by model distance: nonbonded pdb=" OG SER A 139 " pdb=" OE1 GLU A 142 " model vdw 2.075 3.040 nonbonded pdb=" O ASP A 169 " pdb=" OG SER A 173 " model vdw 2.117 3.040 nonbonded pdb=" NH2 ARG A 79 " pdb=" O GLY D 272 " model vdw 2.215 3.120 nonbonded pdb=" O ASP C 76 " pdb=" OG SER C 79 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR B 11 " pdb=" OG1 THR B 43 " model vdw 2.244 3.040 ... (remaining 69959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 196 or (resid 197 through 198 and ( \ name N or name CA or name C or name O or name CB )) or resid 199 through 301)) selection = (chain 'B' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 through 301)) } ncs_group { reference = (chain 'C' and ((resid 63 through 65 and (name N or name CA or name C or name O \ or name CB )) or resid 66 through 74 or (resid 75 through 76 and (name N or name \ CA or name C or name O or name CB )) or resid 77 through 220 or (resid 221 thro \ ugh 223 and (name N or name CA or name C or name O or name CB )) or resid 224 th \ rough 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) \ or resid 228 through 229 or (resid 230 through 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 232 or (resid 233 through 234 and (name N \ or name CA or name C or name O or name CB )) or resid 235 through 307 or (resid \ 308 through 319 and (name N or name CA or name C or name O or name CB )) or (res \ id 320 through 326 and (name N or name CA or name C or name O or name CB )) or r \ esid 327 through 331 or (resid 332 and (name N or name CA or name C or name O or \ name CB )) or resid 333 through 353 or (resid 354 and (name N or name CA or nam \ e C or name O or name CB )) or resid 355 through 359 or (resid 360 through 361 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 63 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 105 or (resid 106 and (name N or n \ ame CA or name C or name O or name CB )) or resid 107 through 108 or (resid 109 \ through 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 218 or (resid 219 through 223 and (name N or name CA or name C or name \ O or name CB )) or resid 224 through 233 or (resid 234 and (name N or name CA o \ r name C or name O or name CB )) or resid 235 through 256 or (resid 257 and (nam \ e N or name CA or name C or name O or name CB )) or resid 258 through 262 or (re \ sid 263 and (name N or name CA or name C or name O or name CB )) or resid 264 th \ rough 301 or (resid 302 and (name N or name CA or name C or name O or name CB )) \ or resid 303 through 333 or (resid 334 and (name N or name CA or name C or name \ O or name CB )) or resid 335 through 361)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.680 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 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 : 0.007 0.063 9223 Z= 0.338 Angle : 0.798 12.378 12637 Z= 0.487 Chirality : 0.050 0.328 1562 Planarity : 0.005 0.090 1674 Dihedral : 16.177 84.942 2846 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.62 % Favored : 89.53 % Rotamer: Outliers : 1.47 % Allowed : 27.36 % Favored : 71.17 % 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 aren not related in a simple way. whole: -0.94 (0.23), residues: 1416 helix: 0.81 (0.19), residues: 766 sheet: -2.27 (0.51), residues: 68 loop : -2.46 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 233 TYR 0.008 0.001 TYR C 68 PHE 0.018 0.002 PHE B 23 TRP 0.012 0.002 TRP D 345 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00667 ( 9223) covalent geometry : angle 0.79838 (12637) hydrogen bonds : bond 0.16783 ( 628) hydrogen bonds : angle 6.80848 ( 1839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.314 Fit side-chains REVERT: A 71 ASN cc_start: 0.8147 (m-40) cc_final: 0.7845 (t0) REVERT: C 306 LEU cc_start: 0.6695 (mt) cc_final: 0.6360 (pp) outliers start: 9 outliers final: 2 residues processed: 139 average time/residue: 0.1563 time to fit residues: 27.2427 Evaluate side-chains 104 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 221 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.224026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.185617 restraints weight = 30752.927| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 3.55 r_work: 0.3329 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9223 Z= 0.230 Angle : 0.695 12.157 12637 Z= 0.357 Chirality : 0.043 0.218 1562 Planarity : 0.005 0.062 1674 Dihedral : 8.923 88.382 1549 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.48 % Favored : 91.10 % Rotamer: Outliers : 7.17 % Allowed : 22.15 % Favored : 70.68 % 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 aren not related in a simple way. whole: -0.65 (0.22), residues: 1416 helix: 1.17 (0.19), residues: 765 sheet: -2.51 (0.52), residues: 77 loop : -2.44 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 53 TYR 0.021 0.002 TYR C 105 PHE 0.014 0.002 PHE A 23 TRP 0.016 0.002 TRP A 60 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 9223) covalent geometry : angle 0.69537 (12637) hydrogen bonds : bond 0.06108 ( 628) hydrogen bonds : angle 5.38431 ( 1839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.351 Fit side-chains REVERT: A 71 ASN cc_start: 0.8508 (m-40) cc_final: 0.7758 (t0) REVERT: A 84 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7808 (pt) REVERT: B 53 ARG cc_start: 0.8796 (ttm170) cc_final: 0.8398 (mtm180) REVERT: B 207 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7621 (tmm) REVERT: C 68 TYR cc_start: 0.7928 (t80) cc_final: 0.7687 (t80) REVERT: C 319 PHE cc_start: 0.6283 (t80) cc_final: 0.5964 (t80) REVERT: C 355 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.6221 (t-90) REVERT: D 79 SER cc_start: 0.8536 (p) cc_final: 0.8322 (p) REVERT: D 241 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7464 (mp) REVERT: D 268 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: D 302 GLU cc_start: 0.6501 (tm-30) cc_final: 0.6163 (tp30) outliers start: 44 outliers final: 22 residues processed: 154 average time/residue: 0.1183 time to fit residues: 24.2369 Evaluate side-chains 135 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 85 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 78 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.223394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170596 restraints weight = 33353.297| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 10.66 r_work: 0.3025 rms_B_bonded: 6.39 restraints_weight: 2.0000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9223 Z= 0.172 Angle : 0.607 11.556 12637 Z= 0.312 Chirality : 0.041 0.152 1562 Planarity : 0.004 0.053 1674 Dihedral : 8.346 89.095 1547 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.19 % Favored : 92.38 % Rotamer: Outliers : 6.19 % Allowed : 22.31 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.23), residues: 1416 helix: 1.45 (0.19), residues: 771 sheet: -1.70 (0.54), residues: 68 loop : -2.26 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 262 TYR 0.014 0.001 TYR C 105 PHE 0.020 0.002 PHE C 247 TRP 0.013 0.002 TRP D 345 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9223) covalent geometry : angle 0.60740 (12637) hydrogen bonds : bond 0.05163 ( 628) hydrogen bonds : angle 5.02484 ( 1839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.398 Fit side-chains REVERT: A 83 MET cc_start: 0.8840 (ptt) cc_final: 0.7881 (ttt) REVERT: C 68 TYR cc_start: 0.7921 (t80) cc_final: 0.7610 (t80) REVERT: C 319 PHE cc_start: 0.5618 (t80) cc_final: 0.5281 (t80) REVERT: D 79 SER cc_start: 0.8343 (p) cc_final: 0.8104 (p) REVERT: D 241 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7424 (mp) REVERT: D 268 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7938 (tt0) outliers start: 38 outliers final: 24 residues processed: 138 average time/residue: 0.1235 time to fit residues: 22.6877 Evaluate side-chains 125 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 101 optimal weight: 0.3980 chunk 129 optimal weight: 30.0000 chunk 121 optimal weight: 50.0000 chunk 117 optimal weight: 40.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.221125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.185812 restraints weight = 37561.574| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 3.06 r_work: 0.3370 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9223 Z= 0.223 Angle : 0.662 11.381 12637 Z= 0.337 Chirality : 0.043 0.217 1562 Planarity : 0.004 0.055 1674 Dihedral : 8.432 83.659 1547 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.62 % Favored : 91.95 % Rotamer: Outliers : 7.65 % Allowed : 21.01 % Favored : 71.34 % 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 aren not related in a simple way. whole: -0.16 (0.23), residues: 1416 helix: 1.43 (0.19), residues: 776 sheet: -0.98 (0.63), residues: 60 loop : -2.26 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.007 0.001 TYR B 205 PHE 0.031 0.002 PHE C 247 TRP 0.017 0.002 TRP D 345 HIS 0.005 0.002 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 9223) covalent geometry : angle 0.66224 (12637) hydrogen bonds : bond 0.05613 ( 628) hydrogen bonds : angle 4.97313 ( 1839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 106 time to evaluate : 0.386 Fit side-chains REVERT: A 83 MET cc_start: 0.8510 (ptt) cc_final: 0.7747 (ttt) REVERT: A 87 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: A 208 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8359 (mt) REVERT: B 207 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7378 (tmm) REVERT: C 68 TYR cc_start: 0.8005 (t80) cc_final: 0.7705 (t80) REVERT: C 319 PHE cc_start: 0.5911 (t80) cc_final: 0.5474 (t80) REVERT: C 355 HIS cc_start: 0.6701 (OUTLIER) cc_final: 0.6355 (t-90) REVERT: D 241 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7519 (mp) REVERT: D 268 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: D 302 GLU cc_start: 0.6672 (tp30) cc_final: 0.6444 (tp30) outliers start: 47 outliers final: 29 residues processed: 142 average time/residue: 0.1125 time to fit residues: 21.7669 Evaluate side-chains 140 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 MET Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 52 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 108 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 57 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 40.0000 chunk 92 optimal weight: 0.0770 chunk 115 optimal weight: 50.0000 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.224015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.189178 restraints weight = 36164.245| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.11 r_work: 0.3418 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9223 Z= 0.141 Angle : 0.569 11.761 12637 Z= 0.292 Chirality : 0.040 0.147 1562 Planarity : 0.003 0.051 1674 Dihedral : 7.905 85.097 1547 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.05 % Favored : 92.52 % Rotamer: Outliers : 5.54 % Allowed : 22.96 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.23), residues: 1416 helix: 1.65 (0.19), residues: 776 sheet: -1.84 (0.54), residues: 80 loop : -2.12 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.004 0.001 TYR C 102 PHE 0.023 0.001 PHE C 247 TRP 0.011 0.001 TRP D 345 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9223) covalent geometry : angle 0.56861 (12637) hydrogen bonds : bond 0.04619 ( 628) hydrogen bonds : angle 4.74627 ( 1839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.299 Fit side-chains REVERT: A 83 MET cc_start: 0.8507 (ptt) cc_final: 0.7810 (ttt) REVERT: A 183 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7606 (t80) REVERT: A 208 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8225 (mt) REVERT: C 68 TYR cc_start: 0.8007 (t80) cc_final: 0.7702 (t80) REVERT: C 342 MET cc_start: 0.8522 (mmm) cc_final: 0.8279 (mmt) REVERT: D 241 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7553 (mp) REVERT: D 268 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7785 (tt0) outliers start: 34 outliers final: 25 residues processed: 124 average time/residue: 0.1169 time to fit residues: 19.3024 Evaluate side-chains 126 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 0.0570 chunk 82 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 50.0000 chunk 15 optimal weight: 0.5980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS C 107 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.224899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.188445 restraints weight = 33509.124| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.76 r_work: 0.3349 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9223 Z= 0.128 Angle : 0.551 12.097 12637 Z= 0.282 Chirality : 0.039 0.159 1562 Planarity : 0.003 0.052 1674 Dihedral : 7.721 87.166 1547 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.77 % Favored : 92.81 % Rotamer: Outliers : 6.35 % Allowed : 21.82 % Favored : 71.82 % 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 aren not related in a simple way. whole: 0.31 (0.23), residues: 1416 helix: 1.88 (0.19), residues: 776 sheet: -1.64 (0.56), residues: 81 loop : -2.04 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 115 TYR 0.005 0.001 TYR D 68 PHE 0.019 0.001 PHE C 247 TRP 0.011 0.001 TRP D 345 HIS 0.004 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9223) covalent geometry : angle 0.55066 (12637) hydrogen bonds : bond 0.04321 ( 628) hydrogen bonds : angle 4.54599 ( 1839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.341 Fit side-chains REVERT: A 83 MET cc_start: 0.8583 (ptt) cc_final: 0.7832 (ttt) REVERT: A 183 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7666 (t80) REVERT: C 68 TYR cc_start: 0.7980 (t80) cc_final: 0.7734 (t80) REVERT: C 95 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8467 (tt) REVERT: C 307 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8093 (ttp-170) REVERT: C 342 MET cc_start: 0.8575 (mmm) cc_final: 0.8321 (mmt) REVERT: D 268 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7852 (tt0) outliers start: 39 outliers final: 26 residues processed: 128 average time/residue: 0.1180 time to fit residues: 20.1888 Evaluate side-chains 126 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 45 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 50.0000 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.220773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.181609 restraints weight = 37554.766| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 3.58 r_work: 0.3293 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9223 Z= 0.240 Angle : 0.669 11.821 12637 Z= 0.337 Chirality : 0.044 0.218 1562 Planarity : 0.004 0.054 1674 Dihedral : 8.385 86.994 1547 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.26 % Favored : 92.31 % Rotamer: Outliers : 7.00 % Allowed : 21.99 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.23), residues: 1416 helix: 1.74 (0.19), residues: 776 sheet: -1.25 (0.61), residues: 72 loop : -2.18 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 53 TYR 0.008 0.001 TYR B 205 PHE 0.018 0.002 PHE C 247 TRP 0.016 0.002 TRP D 345 HIS 0.006 0.002 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 9223) covalent geometry : angle 0.66936 (12637) hydrogen bonds : bond 0.05494 ( 628) hydrogen bonds : angle 4.65987 ( 1839) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.348 Fit side-chains REVERT: A 87 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: A 183 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7543 (t80) REVERT: B 51 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8511 (mm) REVERT: B 207 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7527 (tmm) REVERT: C 68 TYR cc_start: 0.7991 (t80) cc_final: 0.7739 (t80) REVERT: C 95 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8498 (tt) REVERT: C 354 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7867 (tm-30) REVERT: D 241 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7188 (mp) REVERT: D 268 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7876 (tt0) outliers start: 43 outliers final: 30 residues processed: 140 average time/residue: 0.1141 time to fit residues: 21.5721 Evaluate side-chains 143 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 16 optimal weight: 0.0980 chunk 117 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 51 optimal weight: 20.0000 overall best weight: 0.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.224890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176634 restraints weight = 30825.487| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 9.28 r_work: 0.3093 rms_B_bonded: 6.60 restraints_weight: 2.0000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9223 Z= 0.122 Angle : 0.543 11.818 12637 Z= 0.278 Chirality : 0.039 0.207 1562 Planarity : 0.003 0.053 1674 Dihedral : 7.667 89.789 1547 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.62 % Favored : 92.95 % Rotamer: Outliers : 5.37 % Allowed : 23.78 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.23), residues: 1416 helix: 1.97 (0.19), residues: 780 sheet: -1.42 (0.58), residues: 81 loop : -2.00 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 115 TYR 0.003 0.000 TYR C 102 PHE 0.017 0.001 PHE D 247 TRP 0.012 0.001 TRP D 345 HIS 0.004 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9223) covalent geometry : angle 0.54291 (12637) hydrogen bonds : bond 0.04162 ( 628) hydrogen bonds : angle 4.42048 ( 1839) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.284 Fit side-chains REVERT: A 83 MET cc_start: 0.8860 (ptt) cc_final: 0.7956 (ttt) REVERT: A 183 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7718 (t80) REVERT: C 68 TYR cc_start: 0.7976 (t80) cc_final: 0.7751 (t80) REVERT: C 95 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8419 (tt) REVERT: C 306 LEU cc_start: 0.6401 (mt) cc_final: 0.5561 (pp) REVERT: C 342 MET cc_start: 0.8733 (mmm) cc_final: 0.8493 (mmt) REVERT: D 268 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8057 (tt0) outliers start: 33 outliers final: 24 residues processed: 126 average time/residue: 0.1136 time to fit residues: 19.1093 Evaluate side-chains 127 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 78 optimal weight: 20.0000 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN D 107 ASN D 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.223234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.187261 restraints weight = 42187.615| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 3.09 r_work: 0.3388 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9223 Z= 0.157 Angle : 0.584 11.674 12637 Z= 0.296 Chirality : 0.041 0.192 1562 Planarity : 0.003 0.054 1674 Dihedral : 7.851 83.332 1547 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.70 % Favored : 92.95 % Rotamer: Outliers : 5.54 % Allowed : 23.94 % Favored : 70.52 % 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 aren not related in a simple way. whole: 0.47 (0.23), residues: 1416 helix: 2.00 (0.19), residues: 781 sheet: -1.38 (0.59), residues: 80 loop : -2.01 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.005 0.001 TYR B 205 PHE 0.018 0.001 PHE C 247 TRP 0.013 0.001 TRP D 345 HIS 0.005 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9223) covalent geometry : angle 0.58366 (12637) hydrogen bonds : bond 0.04631 ( 628) hydrogen bonds : angle 4.39512 ( 1839) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.315 Fit side-chains REVERT: A 90 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8349 (pp) REVERT: A 92 MET cc_start: 0.8746 (mmm) cc_final: 0.8523 (mmt) REVERT: A 183 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7573 (t80) REVERT: C 68 TYR cc_start: 0.7981 (t80) cc_final: 0.7731 (t80) REVERT: C 306 LEU cc_start: 0.6447 (mt) cc_final: 0.5638 (pp) REVERT: C 342 MET cc_start: 0.8564 (mmm) cc_final: 0.8317 (mmt) REVERT: C 354 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 268 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7802 (tt0) outliers start: 34 outliers final: 27 residues processed: 125 average time/residue: 0.1126 time to fit residues: 18.7989 Evaluate side-chains 131 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 50.0000 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.218388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.179198 restraints weight = 36902.418| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.82 r_work: 0.3228 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 9223 Z= 0.376 Angle : 0.802 11.188 12637 Z= 0.400 Chirality : 0.050 0.287 1562 Planarity : 0.005 0.056 1674 Dihedral : 8.615 86.364 1547 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.55 % Favored : 92.09 % Rotamer: Outliers : 5.54 % Allowed : 24.10 % Favored : 70.36 % 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 aren not related in a simple way. whole: 0.03 (0.23), residues: 1416 helix: 1.63 (0.19), residues: 779 sheet: -1.35 (0.60), residues: 73 loop : -2.23 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 53 TYR 0.012 0.002 TYR B 205 PHE 0.020 0.003 PHE A 23 TRP 0.018 0.003 TRP D 345 HIS 0.010 0.002 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00942 ( 9223) covalent geometry : angle 0.80218 (12637) hydrogen bonds : bond 0.06444 ( 628) hydrogen bonds : angle 4.65507 ( 1839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.350 Fit side-chains REVERT: A 83 MET cc_start: 0.8683 (ptt) cc_final: 0.7807 (ttt) REVERT: B 207 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7740 (tmm) REVERT: B 212 ASP cc_start: 0.8114 (t70) cc_final: 0.7885 (t0) REVERT: C 319 PHE cc_start: 0.6042 (t80) cc_final: 0.5620 (t80) REVERT: C 354 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7934 (tm-30) REVERT: D 268 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8028 (tt0) outliers start: 34 outliers final: 26 residues processed: 132 average time/residue: 0.1168 time to fit residues: 20.6255 Evaluate side-chains 134 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 355 HIS Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 358 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 81 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 12 optimal weight: 0.0980 chunk 82 optimal weight: 0.0770 chunk 34 optimal weight: 0.0980 chunk 126 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 HIS D 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.224528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.187412 restraints weight = 36112.771| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 3.77 r_work: 0.3359 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9223 Z= 0.121 Angle : 0.566 12.055 12637 Z= 0.292 Chirality : 0.040 0.242 1562 Planarity : 0.003 0.052 1674 Dihedral : 7.823 81.649 1547 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.34 % Favored : 93.30 % Rotamer: Outliers : 3.42 % Allowed : 26.38 % Favored : 70.20 % 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 aren not related in a simple way. whole: 0.45 (0.23), residues: 1416 helix: 1.99 (0.19), residues: 781 sheet: -1.47 (0.57), residues: 80 loop : -2.02 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 53 TYR 0.005 0.001 TYR D 68 PHE 0.016 0.001 PHE C 247 TRP 0.014 0.001 TRP D 345 HIS 0.004 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9223) covalent geometry : angle 0.56571 (12637) hydrogen bonds : bond 0.04255 ( 628) hydrogen bonds : angle 4.35580 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.16 seconds wall clock time: 56 minutes 2.93 seconds (3362.93 seconds total)