Starting phenix.real_space_refine on Fri Feb 14 03:34:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fii_31598/02_2025/7fii_31598.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fii_31598/02_2025/7fii_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_31598/02_2025/7fii_31598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fii_31598/02_2025/7fii_31598.map" model { file = "/net/cci-nas-00/data/ceres_data/7fii_31598/02_2025/7fii_31598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fii_31598/02_2025/7fii_31598.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 16, 'ASP:plan': 25, 'TYR:plan': 9, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 8, 'GLU:plan': 19, 'ARG:plan': 25} 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: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 12, 'ASP:plan': 26, 'ASN%COO:plan1': 1, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 19} 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, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} 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: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 14, 'ASN:plan1': 27, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 21, 'GLU:plan': 24, 'ARG:plan': 17} 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, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG: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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 134 Time building chain proxies: 5.79, per 1000 atoms: 0.66 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: 2.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.11 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: 2.80 Time building geometry restraints manager: 2.72 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.740 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- 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 8866 Z= 0.110 Angle : 0.360 5.073 12250 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 : 1.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.000 TRP R 465 HIS 0.002 0.000 HIS A 324 PHE 0.005 0.000 PHE B 235 TYR 0.008 0.001 TYR B 105 ARG 0.009 0.001 ARG A 31 *********************** 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 : 0.980 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1241 time to fit residues: 20.0570 Evaluate side-chains 74 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 38 optimal weight: 40.0000 chunk 76 optimal weight: 50.0000 chunk 60 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 135 optimal weight: 50.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 311 HIS R 429 HIS R 466 HIS R 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.086508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061750 restraints weight = 34216.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063284 restraints weight = 21063.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064326 restraints weight = 15110.114| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 8866 Z= 0.421 Angle : 0.626 7.916 12250 Z= 0.360 Chirality : 0.045 0.195 1572 Planarity : 0.004 0.053 1659 Dihedral : 4.285 28.098 1553 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.84 % Allowed : 11.24 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1508 helix: 2.26 (0.23), residues: 511 sheet: 0.17 (0.32), residues: 276 loop : 0.39 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP B 82 HIS 0.018 0.003 HIS B 54 PHE 0.038 0.003 PHE R 611 TYR 0.031 0.003 TYR R 527 ARG 0.007 0.001 ARG A 31 *********************** 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 82 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 1.000 Fit side-chains REVERT: B 262 MET cc_start: 0.8415 (mpp) cc_final: 0.7933 (mpp) outliers start: 3 outliers final: 2 residues processed: 82 average time/residue: 0.1338 time to fit residues: 18.1824 Evaluate side-chains 68 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 90 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 118 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 14 optimal weight: 40.0000 chunk 120 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 197 HIS R 535 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.089175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066993 restraints weight = 33429.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066718 restraints weight = 25251.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066899 restraints weight = 23028.445| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8866 Z= 0.159 Angle : 0.419 7.272 12250 Z= 0.237 Chirality : 0.040 0.128 1572 Planarity : 0.002 0.032 1659 Dihedral : 3.329 22.931 1553 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.23), residues: 1508 helix: 2.70 (0.23), residues: 520 sheet: -0.02 (0.32), residues: 281 loop : 0.58 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR R 527 ARG 0.002 0.000 ARG A 35 *********************** 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 98 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.943 Fit side-chains REVERT: A 188 LYS cc_start: 0.8571 (mptt) cc_final: 0.8287 (mmtm) REVERT: A 222 ILE cc_start: 0.8713 (mp) cc_final: 0.8440 (tt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1527 time to fit residues: 23.3658 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 : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 105 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.085430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.060973 restraints weight = 34208.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.062595 restraints weight = 20682.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063595 restraints weight = 14704.571| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8866 Z= 0.330 Angle : 0.528 8.515 12250 Z= 0.302 Chirality : 0.043 0.141 1572 Planarity : 0.003 0.034 1659 Dihedral : 3.900 28.099 1553 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1508 helix: 2.20 (0.24), residues: 520 sheet: -0.41 (0.32), residues: 269 loop : 0.25 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 99 HIS 0.008 0.002 HIS B 54 PHE 0.027 0.002 PHE A 240 TYR 0.016 0.002 TYR A 327 ARG 0.004 0.001 ARG B 49 *********************** 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 86 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.989 Fit side-chains REVERT: A 188 LYS cc_start: 0.8724 (mptt) cc_final: 0.8439 (mmtm) REVERT: A 222 ILE cc_start: 0.8701 (mp) cc_final: 0.8422 (tt) REVERT: B 188 MET cc_start: 0.8534 (mmt) cc_final: 0.8114 (mmt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1437 time to fit residues: 19.8080 Evaluate side-chains 66 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 95 optimal weight: 0.3980 chunk 136 optimal weight: 40.0000 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 94 optimal weight: 40.0000 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062592 restraints weight = 34142.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.063595 restraints weight = 23411.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.063641 restraints weight = 18016.285| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8866 Z= 0.277 Angle : 0.491 8.639 12250 Z= 0.279 Chirality : 0.042 0.137 1572 Planarity : 0.003 0.034 1659 Dihedral : 3.859 25.087 1553 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1508 helix: 2.32 (0.23), residues: 512 sheet: -0.70 (0.31), residues: 274 loop : 0.13 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.009 0.002 HIS B 54 PHE 0.022 0.002 PHE A 240 TYR 0.013 0.002 TYR A 230 ARG 0.006 0.001 ARG A 208 *********************** 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 90 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.912 Fit side-chains REVERT: A 188 LYS cc_start: 0.8775 (mptt) cc_final: 0.8537 (mmtm) REVERT: B 188 MET cc_start: 0.8531 (mmt) cc_final: 0.8176 (mmt) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1554 time to fit residues: 21.9310 Evaluate side-chains 66 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 76 optimal weight: 0.5980 chunk 77 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 98 optimal weight: 50.0000 chunk 108 optimal weight: 0.1980 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 143 optimal weight: 0.1980 chunk 99 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.085591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061284 restraints weight = 33424.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063062 restraints weight = 19583.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064258 restraints weight = 13508.483| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 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 = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8866 Z= 0.212 Angle : 0.465 9.251 12250 Z= 0.257 Chirality : 0.041 0.145 1572 Planarity : 0.002 0.033 1659 Dihedral : 3.619 25.709 1553 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1508 helix: 2.57 (0.24), residues: 515 sheet: -0.87 (0.30), residues: 289 loop : 0.13 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.015 0.001 PHE A 240 TYR 0.018 0.001 TYR B 105 ARG 0.005 0.001 ARG A 208 *********************** 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 95 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.082 Fit side-chains REVERT: A 188 LYS cc_start: 0.8736 (mptt) cc_final: 0.8519 (mmtt) REVERT: A 222 ILE cc_start: 0.8741 (mp) cc_final: 0.8484 (tt) REVERT: B 79 LEU cc_start: 0.9181 (mp) cc_final: 0.8597 (mp) REVERT: B 105 TYR cc_start: 0.6948 (t80) cc_final: 0.6550 (t80) REVERT: R 487 MET cc_start: 0.8406 (mmm) cc_final: 0.8121 (tmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1469 time to fit residues: 22.4130 Evaluate side-chains 65 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 118 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 89 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 80 optimal weight: 50.0000 chunk 102 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 45 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 619 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.084655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.062786 restraints weight = 33794.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.062487 restraints weight = 24168.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063004 restraints weight = 19525.278| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8866 Z= 0.266 Angle : 0.494 9.386 12250 Z= 0.278 Chirality : 0.042 0.142 1572 Planarity : 0.003 0.034 1659 Dihedral : 3.797 26.586 1553 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1508 helix: 2.41 (0.24), residues: 518 sheet: -1.01 (0.29), residues: 307 loop : 0.08 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.009 0.001 HIS B 54 PHE 0.020 0.002 PHE A 240 TYR 0.014 0.002 TYR B 105 ARG 0.005 0.001 ARG A 31 *********************** 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 93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.930 Fit side-chains REVERT: A 188 LYS cc_start: 0.8852 (mptt) cc_final: 0.8538 (mmtt) REVERT: A 222 ILE cc_start: 0.8861 (mp) cc_final: 0.8631 (tt) REVERT: R 487 MET cc_start: 0.8418 (mmm) cc_final: 0.8044 (tmm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1454 time to fit residues: 21.6083 Evaluate side-chains 66 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 13 optimal weight: 50.0000 chunk 132 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.0010 chunk 91 optimal weight: 50.0000 chunk 125 optimal weight: 0.0010 chunk 89 optimal weight: 30.0000 chunk 50 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 overall best weight: 1.0174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 619 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.086591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.064546 restraints weight = 33677.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064663 restraints weight = 22377.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064987 restraints weight = 17381.948| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8866 Z= 0.129 Angle : 0.435 10.672 12250 Z= 0.234 Chirality : 0.041 0.133 1572 Planarity : 0.002 0.034 1659 Dihedral : 3.314 22.297 1553 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1508 helix: 2.85 (0.23), residues: 515 sheet: -0.96 (0.30), residues: 289 loop : 0.24 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR R 527 ARG 0.005 0.001 ARG A 208 *********************** 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 99 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.962 Fit side-chains REVERT: A 188 LYS cc_start: 0.8785 (mptt) cc_final: 0.8442 (mmtt) REVERT: A 222 ILE cc_start: 0.8805 (mp) cc_final: 0.8581 (tt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1521 time to fit residues: 23.8851 Evaluate side-chains 66 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 19 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 15 optimal weight: 40.0000 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 94 optimal weight: 40.0000 chunk 64 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.087194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.063073 restraints weight = 33054.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.064885 restraints weight = 19059.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066078 restraints weight = 13059.559| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8866 Z= 0.120 Angle : 0.428 11.009 12250 Z= 0.228 Chirality : 0.040 0.134 1572 Planarity : 0.002 0.034 1659 Dihedral : 3.159 24.024 1553 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.23), residues: 1508 helix: 3.06 (0.23), residues: 509 sheet: -0.81 (0.30), residues: 289 loop : 0.31 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.010 0.001 PHE B 199 TYR 0.014 0.001 TYR R 527 ARG 0.005 0.001 ARG A 31 *********************** 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 96 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.054 Fit side-chains REVERT: A 188 LYS cc_start: 0.8674 (mptt) cc_final: 0.8362 (mmtt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1415 time to fit residues: 22.1036 Evaluate side-chains 66 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2138 > 50: distance: 18 - 21: 23.920 distance: 21 - 22: 16.919 distance: 22 - 23: 21.317 distance: 22 - 25: 9.438 distance: 23 - 24: 11.837 distance: 23 - 26: 32.814 distance: 26 - 27: 17.673 distance: 27 - 28: 32.359 distance: 27 - 30: 44.883 distance: 28 - 29: 19.614 distance: 28 - 31: 28.628 distance: 32 - 33: 9.296 distance: 33 - 34: 8.546 distance: 33 - 36: 51.388 distance: 36 - 37: 40.055 distance: 37 - 38: 25.322 distance: 38 - 39: 46.046 distance: 38 - 41: 28.476 distance: 41 - 42: 10.757 distance: 42 - 43: 22.604 distance: 42 - 45: 19.675 distance: 43 - 44: 6.118 distance: 43 - 46: 34.010 distance: 46 - 47: 20.983 distance: 47 - 50: 11.404 distance: 48 - 49: 33.020 distance: 48 - 51: 20.271 distance: 51 - 52: 9.999 distance: 52 - 53: 12.826 distance: 53 - 54: 20.869 distance: 53 - 55: 24.154 distance: 55 - 56: 29.153 distance: 56 - 57: 9.327 distance: 56 - 59: 9.540 distance: 57 - 58: 32.202 distance: 57 - 60: 4.019 distance: 60 - 61: 12.800 distance: 61 - 62: 16.887 distance: 61 - 64: 26.110 distance: 62 - 63: 34.993 distance: 62 - 65: 6.390 distance: 65 - 66: 23.432 distance: 66 - 67: 20.868 distance: 66 - 69: 37.327 distance: 67 - 68: 17.994 distance: 67 - 70: 29.048