Starting phenix.real_space_refine on Wed Mar 4 01:03:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fii_31598/03_2026/7fii_31598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fii_31598/03_2026/7fii_31598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fii_31598/03_2026/7fii_31598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fii_31598/03_2026/7fii_31598.map" model { file = "/net/cci-nas-00/data/ceres_data/7fii_31598/03_2026/7fii_31598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fii_31598/03_2026/7fii_31598.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1206 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5458 2.51 5 N 1616 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8765 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2131 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 222} Link IDs: {'PTRANS': 8, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 828 Unresolved non-hydrogen angles: 1041 Unresolved non-hydrogen dihedrals: 675 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 25, 'ARG:plan': 25, 'GLN:plan1': 16, 'ASN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 9, 'PHE:plan': 8, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 511 Chain: "B" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2060 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 699 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 26, 'GLN:plan1': 10, 'ARG:plan': 19, 'ASN:plan1': 12, 'TYR:plan': 1, 'HIS:plan': 4, 'PHE:plan': 4, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 335 Chain: "G" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 307 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "R" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3262 Classifications: {'peptide': 570} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 371} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 541} Chain breaks: 1 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1295 Unresolved non-hydrogen angles: 1658 Unresolved non-hydrogen dihedrals: 1055 Unresolved non-hydrogen chiralities: 148 Planarities with less than four sites: {'GLU:plan': 24, 'ASN:plan1': 27, 'ASP:plan': 14, 'ARG:plan': 17, 'TYR:plan': 14, 'GLN:plan1': 12, 'PHE:plan': 21, 'HIS:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 613 Chain: "X" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 450 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 6, 'TRANS': 81} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'PHE:plan': 4, 'ARG:plan': 3, 'TYR:plan': 4, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 133 Chain: "Y" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 555 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 10, 'ASN:plan1': 4, 'TYR:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 134 Time building chain proxies: 2.37, per 1000 atoms: 0.27 Number of scatterers: 8765 At special positions: 0 Unit cell: (88.893, 95.319, 184.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1643 8.00 N 1616 7.00 C 5458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " distance=2.03 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.03 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 9 " - pdb=" SG CYS Y 57 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 26 " - pdb=" SG CYS Y 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 34 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 38 " - pdb=" SG CYS Y 90 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 93 " - pdb=" SG CYS Y 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 445.8 milliseconds 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 19 sheets defined 36.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.515A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.539A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 91 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.627A pdb=" N ASP A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 151 through 163 removed outlier: 4.728A pdb=" N ASP A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.231A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.722A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.798A pdb=" N ALA A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.509A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 317 Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.610A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.842A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 46 removed outlier: 3.511A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 265 Processing helix chain 'R' and resid 275 through 280 removed outlier: 3.569A pdb=" N CYS R 279 " --> pdb=" O TYR R 275 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS R 280 " --> pdb=" O PRO R 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 275 through 280' Processing helix chain 'R' and resid 361 through 386 removed outlier: 4.312A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 422 Processing helix chain 'R' and resid 425 through 436 removed outlier: 4.628A pdb=" N ILE R 431 " --> pdb=" O TYR R 427 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP R 432 " --> pdb=" O ASN R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 470 removed outlier: 3.956A pdb=" N SER R 440 " --> pdb=" O GLY R 436 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 504 removed outlier: 3.977A pdb=" N LEU R 485 " --> pdb=" O ARG R 481 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE R 486 " --> pdb=" O HIS R 482 " (cutoff:3.500A) Proline residue: R 501 - end of helix removed outlier: 3.511A pdb=" N GLY R 504 " --> pdb=" O LEU R 500 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 554 Processing helix chain 'R' and resid 560 through 594 removed outlier: 3.974A pdb=" N ASP R 578 " --> pdb=" O LEU R 574 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS R 581 " --> pdb=" O THR R 577 " (cutoff:3.500A) Proline residue: R 584 - end of helix Processing helix chain 'R' and resid 600 through 611 removed outlier: 3.703A pdb=" N VAL R 606 " --> pdb=" O THR R 602 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) Processing helix chain 'R' and resid 613 through 624 Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 627 through 642 Processing helix chain 'X' and resid 40 through 46 Processing helix chain 'X' and resid 71 through 73 No H-bonds generated for 'chain 'X' and resid 71 through 73' Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.544A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 198 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 200 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.544A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.934A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 51 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.945A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.581A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.257A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.857A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.181A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.578A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.104A pdb=" N LEU R 54 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE R 151 " --> pdb=" O THR R 178 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS R 180 " --> pdb=" O PHE R 151 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU R 153 " --> pdb=" O LYS R 180 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL R 177 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLU R 203 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU R 179 " --> pdb=" O GLU R 203 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR R 226 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU R 248 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA R 344 " --> pdb=" O ALA R 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 63 through 64 removed outlier: 3.930A pdb=" N ILE R 64 " --> pdb=" O ARG R 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE R 89 " --> pdb=" O TYR R 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 94 through 95 removed outlier: 6.090A pdb=" N PHE R 94 " --> pdb=" O ILE R 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'R' and resid 195 through 197 Processing sheet with id=AB5, first strand: chain 'X' and resid 11 through 14 removed outlier: 3.737A pdb=" N MET X 29 " --> pdb=" O THR X 11 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY X 30 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR Y 40 " --> pdb=" O GLY X 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'X' and resid 35 through 37 removed outlier: 3.638A pdb=" N ARG X 35 " --> pdb=" O GLU X 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 60 through 62 Processing sheet with id=AB8, first strand: chain 'X' and resid 65 through 69 removed outlier: 3.523A pdb=" N VAL X 76 " --> pdb=" O VAL X 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 10 through 18 removed outlier: 3.567A pdb=" N ALA Y 35 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 56 through 68 removed outlier: 5.980A pdb=" N CYS Y 57 " --> pdb=" O CYS Y 90 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS Y 90 " --> pdb=" O CYS Y 57 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR Y 59 " --> pdb=" O CYS Y 88 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N CYS Y 88 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASP Y 61 " --> pdb=" O LEU Y 86 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU Y 86 " --> pdb=" O ASP Y 61 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE Y 67 " --> pdb=" O VAL Y 80 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL Y 80 " --> pdb=" O ILE Y 67 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1410 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: 1.60 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3168 1.35 - 1.46: 2018 1.46 - 1.58: 3621 1.58 - 1.70: 0 1.70 - 1.81: 59 Bond restraints: 8866 Sorted by residual: bond pdb=" N GLU R 32 " pdb=" CA GLU R 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N CYS A 3 " pdb=" CA CYS A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN X 5 " pdb=" CA GLN X 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N LYS Y 2 " pdb=" CA LYS Y 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 8861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 12011 1.01 - 2.03: 206 2.03 - 3.04: 17 3.04 - 4.06: 10 4.06 - 5.07: 6 Bond angle restraints: 12250 Sorted by residual: angle pdb=" N CYS R 581 " pdb=" CA CYS R 581 " pdb=" C CYS R 581 " ideal model delta sigma weight residual 114.62 111.41 3.21 1.14e+00 7.69e-01 7.91e+00 angle pdb=" C THR R 580 " pdb=" N CYS R 581 " pdb=" CA CYS R 581 " ideal model delta sigma weight residual 121.63 126.70 -5.07 1.91e+00 2.74e-01 7.05e+00 angle pdb=" CA ILE B 93 " pdb=" C ILE B 93 " pdb=" O ILE B 93 " ideal model delta sigma weight residual 120.88 119.65 1.23 6.80e-01 2.16e+00 3.26e+00 angle pdb=" CA ASP A 94 " pdb=" C ASP A 94 " pdb=" N PHE A 95 " ideal model delta sigma weight residual 114.76 116.78 -2.02 1.14e+00 7.69e-01 3.15e+00 angle pdb=" CA ILE B 93 " pdb=" C ILE B 93 " pdb=" N PRO B 94 " ideal model delta sigma weight residual 118.12 119.55 -1.43 8.10e-01 1.52e+00 3.11e+00 ... (remaining 12245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4918 16.52 - 33.04: 160 33.04 - 49.55: 34 49.55 - 66.07: 4 66.07 - 82.59: 2 Dihedral angle restraints: 5118 sinusoidal: 716 harmonic: 4402 Sorted by residual: dihedral pdb=" CB CYS X 28 " pdb=" SG CYS X 28 " pdb=" SG CYS X 82 " pdb=" CB CYS X 82 " ideal model delta sinusoidal sigma weight residual 93.00 174.74 -81.74 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS Y 38 " pdb=" SG CYS Y 38 " pdb=" SG CYS Y 90 " pdb=" CB CYS Y 90 " ideal model delta sinusoidal sigma weight residual 93.00 28.21 64.79 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CB CYS R 439 " pdb=" SG CYS R 439 " pdb=" SG CYS R 514 " pdb=" CB CYS R 514 " ideal model delta sinusoidal sigma weight residual -86.00 -126.86 40.86 1 1.00e+01 1.00e-02 2.34e+01 ... (remaining 5115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 936 0.026 - 0.052: 409 0.052 - 0.077: 108 0.077 - 0.103: 54 0.103 - 0.129: 65 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ILE R 64 " pdb=" N ILE R 64 " pdb=" C ILE R 64 " pdb=" CB ILE R 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE R 155 " pdb=" N ILE R 155 " pdb=" C ILE R 155 " pdb=" CB ILE R 155 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE R 80 " pdb=" N ILE R 80 " pdb=" C ILE R 80 " pdb=" CB ILE R 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1569 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 596 " -0.022 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO R 597 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 597 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 597 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 515 " -0.013 5.00e-02 4.00e+02 1.95e-02 6.08e-01 pdb=" N PRO R 516 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO R 516 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 516 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 612 " -0.009 5.00e-02 4.00e+02 1.39e-02 3.09e-01 pdb=" N PRO R 613 " 0.024 5.00e-02 4.00e+02 pdb=" CA PRO R 613 " -0.007 5.00e-02 4.00e+02 pdb=" CD PRO R 613 " -0.008 5.00e-02 4.00e+02 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 37 2.64 - 3.20: 7981 3.20 - 3.77: 12863 3.77 - 4.33: 14620 4.33 - 4.90: 25551 Nonbonded interactions: 61052 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" O THR B 165 " model vdw 2.073 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.138 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.361 3.040 nonbonded pdb=" OE1 GLN A 213 " pdb=" NH1 ARG B 314 " model vdw 2.388 3.120 nonbonded pdb=" O THR A 181 " pdb=" ND2 ASN B 119 " model vdw 2.409 3.120 ... (remaining 61047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8878 Z= 0.090 Angle : 0.360 5.073 12274 Z= 0.219 Chirality : 0.039 0.129 1572 Planarity : 0.001 0.034 1659 Dihedral : 8.974 82.588 2218 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.24), residues: 1508 helix: 3.93 (0.24), residues: 508 sheet: 1.69 (0.39), residues: 208 loop : 0.97 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 31 TYR 0.008 0.001 TYR B 105 PHE 0.005 0.000 PHE B 235 TRP 0.003 0.000 TRP R 465 HIS 0.002 0.000 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00158 ( 8866) covalent geometry : angle 0.35993 (12250) SS BOND : bond 0.00108 ( 12) SS BOND : angle 0.42006 ( 24) hydrogen bonds : bond 0.16745 ( 482) hydrogen bonds : angle 5.91175 ( 1410) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.239 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0634 time to fit residues: 10.1760 Evaluate side-chains 73 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.094063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073056 restraints weight = 32409.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.073587 restraints weight = 23489.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073691 restraints weight = 18118.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.074207 restraints weight = 16301.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.074449 restraints weight = 13530.995| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8878 Z= 0.113 Angle : 0.414 5.993 12274 Z= 0.231 Chirality : 0.040 0.128 1572 Planarity : 0.002 0.027 1659 Dihedral : 2.787 24.282 1553 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.23), residues: 1508 helix: 3.43 (0.24), residues: 501 sheet: 0.80 (0.33), residues: 258 loop : 0.94 (0.25), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TYR 0.012 0.001 TYR R 527 PHE 0.012 0.001 PHE A 199 TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8866) covalent geometry : angle 0.41426 (12250) SS BOND : bond 0.00103 ( 12) SS BOND : angle 0.39080 ( 24) hydrogen bonds : bond 0.02975 ( 482) hydrogen bonds : angle 3.91396 ( 1410) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.326 Fit side-chains REVERT: B 262 MET cc_start: 0.8108 (mpp) cc_final: 0.7644 (mpp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0664 time to fit residues: 10.2708 Evaluate side-chains 76 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 11 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 78 optimal weight: 50.0000 chunk 69 optimal weight: 5.9990 chunk 99 optimal weight: 40.0000 chunk 71 optimal weight: 7.9990 chunk 98 optimal weight: 50.0000 chunk 148 optimal weight: 50.0000 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN R 535 ASN ** R 619 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 = 0.3698 r_free = 0.3698 target = 0.086812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.063092 restraints weight = 33879.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.064771 restraints weight = 22635.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064597 restraints weight = 14976.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065422 restraints weight = 14580.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065182 restraints weight = 12528.400| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8878 Z= 0.212 Angle : 0.531 7.248 12274 Z= 0.306 Chirality : 0.043 0.171 1572 Planarity : 0.003 0.039 1659 Dihedral : 3.793 26.792 1553 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.56 % Allowed : 9.55 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.23), residues: 1508 helix: 2.45 (0.23), residues: 523 sheet: -0.06 (0.32), residues: 271 loop : 0.53 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.021 0.002 TYR R 527 PHE 0.026 0.002 PHE R 611 TRP 0.020 0.003 TRP B 82 HIS 0.012 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8866) covalent geometry : angle 0.53025 (12250) SS BOND : bond 0.00278 ( 12) SS BOND : angle 0.75196 ( 24) hydrogen bonds : bond 0.04197 ( 482) hydrogen bonds : angle 4.16263 ( 1410) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.319 Fit side-chains REVERT: B 188 MET cc_start: 0.8863 (mmp) cc_final: 0.8649 (mmt) REVERT: B 262 MET cc_start: 0.8402 (mpp) cc_final: 0.7952 (mpp) outliers start: 2 outliers final: 1 residues processed: 87 average time/residue: 0.0589 time to fit residues: 8.5593 Evaluate side-chains 61 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 85 optimal weight: 10.0000 chunk 77 optimal weight: 50.0000 chunk 56 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 148 optimal weight: 40.0000 chunk 65 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 96 optimal weight: 40.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 429 HIS ** R 619 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 = 0.3645 r_free = 0.3645 target = 0.084423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059728 restraints weight = 35244.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.061298 restraints weight = 21237.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.062262 restraints weight = 15038.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063000 restraints weight = 12007.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063363 restraints weight = 10291.688| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8878 Z= 0.252 Angle : 0.570 8.836 12274 Z= 0.328 Chirality : 0.044 0.164 1572 Planarity : 0.003 0.036 1659 Dihedral : 4.288 26.797 1553 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1508 helix: 1.76 (0.23), residues: 531 sheet: -0.50 (0.32), residues: 271 loop : 0.10 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.018 0.002 TYR B 85 PHE 0.026 0.002 PHE R 611 TRP 0.017 0.002 TRP B 82 HIS 0.012 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 8866) covalent geometry : angle 0.56816 (12250) SS BOND : bond 0.00565 ( 12) SS BOND : angle 1.13790 ( 24) hydrogen bonds : bond 0.04326 ( 482) hydrogen bonds : angle 4.39655 ( 1410) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.311 Fit side-chains REVERT: A 188 LYS cc_start: 0.8645 (mptt) cc_final: 0.8404 (mmtm) REVERT: A 358 TYR cc_start: 0.8001 (m-10) cc_final: 0.7780 (m-10) REVERT: B 79 LEU cc_start: 0.9210 (mp) cc_final: 0.8684 (mp) REVERT: B 262 MET cc_start: 0.8250 (mpp) cc_final: 0.7860 (mpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0648 time to fit residues: 8.1478 Evaluate side-chains 58 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 111 optimal weight: 0.2980 chunk 99 optimal weight: 50.0000 chunk 98 optimal weight: 50.0000 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 615 ASN R 619 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.059759 restraints weight = 33861.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.061476 restraints weight = 20142.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.062571 restraints weight = 13970.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063175 restraints weight = 10903.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.063803 restraints weight = 9379.750| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8878 Z= 0.190 Angle : 0.499 9.694 12274 Z= 0.282 Chirality : 0.042 0.133 1572 Planarity : 0.003 0.034 1659 Dihedral : 4.005 26.514 1553 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.23), residues: 1508 helix: 2.14 (0.23), residues: 523 sheet: -0.68 (0.30), residues: 300 loop : -0.00 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 208 TYR 0.021 0.002 TYR A 327 PHE 0.015 0.002 PHE R 611 TRP 0.011 0.002 TRP B 169 HIS 0.011 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8866) covalent geometry : angle 0.49846 (12250) SS BOND : bond 0.00230 ( 12) SS BOND : angle 0.82182 ( 24) hydrogen bonds : bond 0.03827 ( 482) hydrogen bonds : angle 4.05779 ( 1410) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.318 Fit side-chains REVERT: A 188 LYS cc_start: 0.8666 (mptt) cc_final: 0.8379 (mmtm) REVERT: B 188 MET cc_start: 0.8535 (mmt) cc_final: 0.8132 (mmt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0691 time to fit residues: 9.1492 Evaluate side-chains 58 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 56 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 38 optimal weight: 0.0270 chunk 143 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 50.0000 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 50.0000 chunk 147 optimal weight: 0.0770 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.087222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.064273 restraints weight = 32929.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065604 restraints weight = 21741.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066166 restraints weight = 15077.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066023 restraints weight = 13289.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.066322 restraints weight = 11496.040| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 8878 Z= 0.098 Angle : 0.441 9.915 12274 Z= 0.241 Chirality : 0.041 0.137 1572 Planarity : 0.002 0.034 1659 Dihedral : 3.443 24.808 1553 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.23), residues: 1508 helix: 2.65 (0.23), residues: 518 sheet: -0.65 (0.31), residues: 283 loop : 0.15 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 208 TYR 0.017 0.001 TYR B 105 PHE 0.015 0.001 PHE A 240 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8866) covalent geometry : angle 0.44030 (12250) SS BOND : bond 0.00086 ( 12) SS BOND : angle 0.60519 ( 24) hydrogen bonds : bond 0.03087 ( 482) hydrogen bonds : angle 3.59619 ( 1410) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.320 Fit side-chains REVERT: A 188 LYS cc_start: 0.8644 (mptt) cc_final: 0.8351 (mmtm) REVERT: A 222 ILE cc_start: 0.8707 (mp) cc_final: 0.8476 (tt) REVERT: A 264 LEU cc_start: 0.8895 (tp) cc_final: 0.8589 (pp) REVERT: B 188 MET cc_start: 0.8437 (mmt) cc_final: 0.8045 (mmp) REVERT: B 262 MET cc_start: 0.8436 (mmm) cc_final: 0.8060 (mmm) REVERT: R 582 MET cc_start: 0.7261 (tmm) cc_final: 0.7059 (tmm) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0640 time to fit residues: 10.0124 Evaluate side-chains 68 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 57 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 86 optimal weight: 0.0010 chunk 15 optimal weight: 40.0000 chunk 28 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 139 optimal weight: 50.0000 chunk 110 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 5.9994 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.082192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.060360 restraints weight = 34768.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.060553 restraints weight = 22804.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.060860 restraints weight = 18748.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.061220 restraints weight = 16141.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.061497 restraints weight = 13691.011| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 8878 Z= 0.275 Angle : 0.599 9.062 12274 Z= 0.339 Chirality : 0.044 0.153 1572 Planarity : 0.003 0.036 1659 Dihedral : 4.351 27.755 1553 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1508 helix: 1.96 (0.23), residues: 526 sheet: -1.00 (0.29), residues: 313 loop : -0.15 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 49 TYR 0.019 0.002 TYR B 105 PHE 0.035 0.002 PHE A 240 TRP 0.012 0.002 TRP B 82 HIS 0.008 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 8866) covalent geometry : angle 0.59750 (12250) SS BOND : bond 0.00341 ( 12) SS BOND : angle 1.12901 ( 24) hydrogen bonds : bond 0.04500 ( 482) hydrogen bonds : angle 4.31398 ( 1410) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.324 Fit side-chains REVERT: A 188 LYS cc_start: 0.8769 (mptt) cc_final: 0.8427 (mmtt) REVERT: B 188 MET cc_start: 0.8581 (mmt) cc_final: 0.8033 (mmt) REVERT: B 262 MET cc_start: 0.8427 (mmm) cc_final: 0.8177 (mmm) REVERT: R 582 MET cc_start: 0.7088 (tmm) cc_final: 0.6884 (tmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0646 time to fit residues: 8.2853 Evaluate side-chains 64 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 114 optimal weight: 0.3980 chunk 56 optimal weight: 30.0000 chunk 139 optimal weight: 50.0000 chunk 13 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 98 optimal weight: 50.0000 chunk 137 optimal weight: 0.8980 chunk 84 optimal weight: 40.0000 chunk 134 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 overall best weight: 3.8586 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.083314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060668 restraints weight = 34023.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.061106 restraints weight = 26163.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061732 restraints weight = 18554.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.062120 restraints weight = 16053.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062098 restraints weight = 13520.345| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8878 Z= 0.181 Angle : 0.515 9.950 12274 Z= 0.286 Chirality : 0.042 0.149 1572 Planarity : 0.003 0.033 1659 Dihedral : 4.042 26.464 1553 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.23), residues: 1508 helix: 2.29 (0.24), residues: 515 sheet: -1.33 (0.28), residues: 304 loop : -0.11 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 208 TYR 0.017 0.002 TYR R 527 PHE 0.022 0.002 PHE A 312 TRP 0.012 0.002 TRP B 169 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8866) covalent geometry : angle 0.51449 (12250) SS BOND : bond 0.00240 ( 12) SS BOND : angle 0.83099 ( 24) hydrogen bonds : bond 0.03749 ( 482) hydrogen bonds : angle 3.98684 ( 1410) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.336 Fit side-chains REVERT: A 188 LYS cc_start: 0.8801 (mptt) cc_final: 0.8543 (mmtm) REVERT: A 222 ILE cc_start: 0.8752 (mp) cc_final: 0.8477 (tt) REVERT: R 582 MET cc_start: 0.7114 (tmm) cc_final: 0.6880 (tmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0671 time to fit residues: 9.5466 Evaluate side-chains 67 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 103 optimal weight: 10.0000 chunk 86 optimal weight: 0.0170 chunk 40 optimal weight: 0.0020 chunk 135 optimal weight: 50.0000 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 40.0000 chunk 147 optimal weight: 0.0170 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 40.0000 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 1.0066 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.085798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.063368 restraints weight = 33216.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064092 restraints weight = 21894.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.064914 restraints weight = 16886.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065017 restraints weight = 15377.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065130 restraints weight = 12474.807| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8878 Z= 0.089 Angle : 0.449 11.298 12274 Z= 0.241 Chirality : 0.041 0.146 1572 Planarity : 0.002 0.035 1659 Dihedral : 3.476 24.599 1553 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1508 helix: 2.74 (0.23), residues: 515 sheet: -1.11 (0.29), residues: 298 loop : 0.05 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.015 0.001 TYR R 527 PHE 0.013 0.001 PHE A 189 TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 8866) covalent geometry : angle 0.44878 (12250) SS BOND : bond 0.00105 ( 12) SS BOND : angle 0.51275 ( 24) hydrogen bonds : bond 0.03036 ( 482) hydrogen bonds : angle 3.60304 ( 1410) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.333 Fit side-chains REVERT: A 188 LYS cc_start: 0.8687 (mptt) cc_final: 0.8351 (mmtm) REVERT: A 222 ILE cc_start: 0.8820 (mp) cc_final: 0.8583 (tt) REVERT: B 188 MET cc_start: 0.8397 (mmt) cc_final: 0.7879 (mmp) REVERT: R 398 MET cc_start: 0.7781 (mmp) cc_final: 0.7334 (tpp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0614 time to fit residues: 9.3378 Evaluate side-chains 68 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 61 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 90 optimal weight: 40.0000 chunk 51 optimal weight: 9.9990 chunk 6 optimal weight: 40.0000 chunk 130 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 50.0000 chunk 114 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.083262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.061494 restraints weight = 34137.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.061551 restraints weight = 23874.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062202 restraints weight = 17890.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062428 restraints weight = 15736.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062493 restraints weight = 13423.543| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8878 Z= 0.188 Angle : 0.516 10.821 12274 Z= 0.286 Chirality : 0.043 0.144 1572 Planarity : 0.003 0.033 1659 Dihedral : 3.873 26.423 1553 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1508 helix: 2.48 (0.24), residues: 515 sheet: -1.23 (0.29), residues: 305 loop : -0.05 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 208 TYR 0.018 0.002 TYR B 105 PHE 0.023 0.002 PHE A 240 TRP 0.027 0.002 TRP B 169 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8866) covalent geometry : angle 0.51538 (12250) SS BOND : bond 0.00226 ( 12) SS BOND : angle 0.75158 ( 24) hydrogen bonds : bond 0.03738 ( 482) hydrogen bonds : angle 3.89629 ( 1410) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.330 Fit side-chains REVERT: A 188 LYS cc_start: 0.8775 (mptt) cc_final: 0.8477 (mmtt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0587 time to fit residues: 8.3920 Evaluate side-chains 64 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 38 optimal weight: 0.0670 chunk 111 optimal weight: 2.9990 chunk 82 optimal weight: 40.0000 chunk 62 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 40.0000 chunk 105 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.9522 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.084747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.062373 restraints weight = 33643.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063128 restraints weight = 22893.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064403 restraints weight = 16681.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.064405 restraints weight = 15155.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064474 restraints weight = 11731.930| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8878 Z= 0.111 Angle : 0.454 11.095 12274 Z= 0.247 Chirality : 0.041 0.137 1572 Planarity : 0.002 0.034 1659 Dihedral : 3.559 24.211 1553 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.23), residues: 1508 helix: 2.67 (0.23), residues: 515 sheet: -1.18 (0.29), residues: 292 loop : 0.00 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.016 0.001 TYR R 527 PHE 0.011 0.001 PHE A 189 TRP 0.027 0.002 TRP B 169 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8866) covalent geometry : angle 0.45378 (12250) SS BOND : bond 0.00137 ( 12) SS BOND : angle 0.56078 ( 24) hydrogen bonds : bond 0.03198 ( 482) hydrogen bonds : angle 3.66894 ( 1410) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.02 seconds wall clock time: 29 minutes 58.44 seconds (1798.44 seconds total)