Starting phenix.real_space_refine on Thu Mar 14 22:42:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/03_2024/7fii_31598.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/03_2024/7fii_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/03_2024/7fii_31598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/03_2024/7fii_31598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/03_2024/7fii_31598.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/03_2024/7fii_31598.pdb" } 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 Residue "A GLU 311": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.58, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 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: 3.30 Conformation dependent library (CDL) restraints added in 2.3 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: 1.15 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: 2.82 Time building geometry restraints manager: 3.63 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: 100.74 - 107.38: 164 107.38 - 114.03: 4982 114.03 - 120.68: 3664 120.68 - 127.33: 3389 127.33 - 133.98: 51 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 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.138 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.361 2.440 nonbonded pdb=" OE1 GLN A 213 " pdb=" NH1 ARG B 314 " model vdw 2.388 2.520 nonbonded pdb=" O THR A 181 " pdb=" ND2 ASN B 119 " model vdw 2.409 2.520 ... (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 ========== 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: 1.150 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: 4.120 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.480 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.110 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.049 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1401 time to fit residues: 22.1317 Evaluate side-chains 74 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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: 5.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 38 optimal weight: 40.0000 chunk 76 optimal weight: 50.0000 chunk 60 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 135 optimal weight: 50.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN R 429 HIS R 466 HIS R 535 ASN R 615 ASN R 619 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 8866 Z= 0.506 Angle : 0.708 9.177 12250 Z= 0.408 Chirality : 0.046 0.221 1572 Planarity : 0.004 0.056 1659 Dihedral : 4.552 28.675 1553 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.12 % Allowed : 12.64 % Favored : 86.24 % 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: 1.14 (0.22), residues: 1508 helix: 1.96 (0.23), residues: 518 sheet: -0.06 (0.31), residues: 275 loop : 0.31 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP B 82 HIS 0.019 0.004 HIS B 54 PHE 0.043 0.003 PHE R 611 TYR 0.033 0.003 TYR R 527 ARG 0.006 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 83 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.023 Fit side-chains REVERT: B 262 MET cc_start: 0.8368 (mpp) cc_final: 0.7975 (mpp) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 0.1332 time to fit residues: 18.3208 Evaluate side-chains 64 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 92 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 0.0970 chunk 146 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 134 optimal weight: 30.0000 chunk 46 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 311 HIS R 615 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8866 Z= 0.107 Angle : 0.411 8.370 12250 Z= 0.227 Chirality : 0.040 0.136 1572 Planarity : 0.002 0.027 1659 Dihedral : 3.209 19.085 1553 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: 1.83 (0.23), residues: 1508 helix: 2.75 (0.23), residues: 519 sheet: 0.12 (0.32), residues: 265 loop : 0.61 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS A 324 PHE 0.012 0.001 PHE A 189 TYR 0.012 0.001 TYR R 527 ARG 0.002 0.001 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 109 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: B 188 MET cc_start: 0.8462 (mmt) cc_final: 0.8024 (mmp) REVERT: B 262 MET cc_start: 0.8359 (mpp) cc_final: 0.8017 (mpp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1498 time to fit residues: 25.1359 Evaluate side-chains 69 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 70 optimal weight: 40.0000 chunk 15 optimal weight: 50.0000 chunk 64 optimal weight: 6.9990 chunk 91 optimal weight: 50.0000 chunk 136 optimal weight: 40.0000 chunk 144 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 8866 Z= 0.485 Angle : 0.664 9.771 12250 Z= 0.382 Chirality : 0.046 0.178 1572 Planarity : 0.004 0.041 1659 Dihedral : 4.818 27.387 1553 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % 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: 0.49 (0.22), residues: 1508 helix: 1.53 (0.23), residues: 525 sheet: -0.75 (0.31), residues: 277 loop : -0.03 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 297 HIS 0.010 0.002 HIS B 54 PHE 0.035 0.003 PHE A 240 TYR 0.025 0.003 TYR B 105 ARG 0.005 0.001 ARG A 31 *********************** 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 73 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.819 Fit side-chains REVERT: A 188 LYS cc_start: 0.8865 (mppt) cc_final: 0.8662 (mmtt) REVERT: B 188 MET cc_start: 0.8562 (mmt) cc_final: 0.7959 (mmt) REVERT: B 262 MET cc_start: 0.8371 (mpp) cc_final: 0.7834 (mpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1391 time to fit residues: 16.5573 Evaluate side-chains 56 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 0.0570 chunk 81 optimal weight: 0.0370 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 73 optimal weight: 0.0000 chunk 129 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 615 ASN R 619 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8866 Z= 0.166 Angle : 0.446 9.459 12250 Z= 0.248 Chirality : 0.041 0.129 1572 Planarity : 0.002 0.032 1659 Dihedral : 3.776 26.118 1553 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: 1.00 (0.23), residues: 1508 helix: 2.34 (0.23), residues: 529 sheet: -0.69 (0.31), residues: 283 loop : 0.04 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.012 0.001 PHE B 222 TYR 0.015 0.001 TYR R 527 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 99 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.030 Fit side-chains REVERT: B 188 MET cc_start: 0.8698 (mmt) cc_final: 0.7931 (mmp) REVERT: B 262 MET cc_start: 0.8341 (mpp) cc_final: 0.8137 (mmm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1466 time to fit residues: 22.6327 Evaluate side-chains 63 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 84 optimal weight: 40.0000 chunk 35 optimal weight: 40.0000 chunk 144 optimal weight: 50.0000 chunk 119 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 40.0000 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 40.0000 overall best weight: 8.1592 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 8866 Z= 0.547 Angle : 0.715 7.843 12250 Z= 0.413 Chirality : 0.048 0.207 1572 Planarity : 0.004 0.056 1659 Dihedral : 5.183 25.583 1553 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -0.20 (0.22), residues: 1508 helix: 1.17 (0.23), residues: 526 sheet: -1.30 (0.29), residues: 299 loop : -0.51 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 82 HIS 0.013 0.003 HIS B 54 PHE 0.041 0.003 PHE A 240 TYR 0.023 0.003 TYR R 455 ARG 0.005 0.001 ARG A 31 *********************** 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 72 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.988 Fit side-chains REVERT: B 82 TRP cc_start: 0.8218 (m100) cc_final: 0.7973 (m100) REVERT: B 188 MET cc_start: 0.8565 (mmt) cc_final: 0.8002 (mmt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1301 time to fit residues: 15.8019 Evaluate side-chains 56 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 0.0030 chunk 16 optimal weight: 7.9990 chunk 82 optimal weight: 50.0000 chunk 105 optimal weight: 0.8980 chunk 81 optimal weight: 50.0000 chunk 121 optimal weight: 50.0000 chunk 80 optimal weight: 9.9990 chunk 143 optimal weight: 50.0000 chunk 89 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 overall best weight: 3.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8866 Z= 0.255 Angle : 0.508 9.887 12250 Z= 0.284 Chirality : 0.042 0.136 1572 Planarity : 0.003 0.037 1659 Dihedral : 4.314 25.336 1553 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: 0.27 (0.23), residues: 1508 helix: 1.95 (0.23), residues: 521 sheet: -1.32 (0.29), residues: 297 loop : -0.42 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 169 HIS 0.007 0.001 HIS B 54 PHE 0.023 0.002 PHE A 312 TYR 0.019 0.002 TYR A 327 ARG 0.004 0.001 ARG A 208 *********************** 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 87 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.096 Fit side-chains REVERT: B 188 MET cc_start: 0.8821 (mmt) cc_final: 0.8193 (mmp) REVERT: B 262 MET cc_start: 0.8442 (mmm) cc_final: 0.8166 (mmm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1597 time to fit residues: 21.5644 Evaluate side-chains 62 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 43 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 91 optimal weight: 50.0000 chunk 97 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 8866 Z= 0.529 Angle : 0.693 10.435 12250 Z= 0.396 Chirality : 0.048 0.234 1572 Planarity : 0.004 0.041 1659 Dihedral : 5.156 27.573 1553 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % 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 (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: -0.44 (0.22), residues: 1508 helix: 1.17 (0.23), residues: 520 sheet: -1.68 (0.30), residues: 279 loop : -0.72 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 169 HIS 0.014 0.003 HIS B 54 PHE 0.037 0.003 PHE A 240 TYR 0.027 0.003 TYR B 85 ARG 0.005 0.001 ARG A 31 *********************** 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 68 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.015 Fit side-chains REVERT: B 188 MET cc_start: 0.8660 (mmt) cc_final: 0.8059 (mmt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1187 time to fit residues: 14.1548 Evaluate side-chains 56 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 9.9990 chunk 137 optimal weight: 40.0000 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 87 optimal weight: 40.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8866 Z= 0.146 Angle : 0.494 11.637 12250 Z= 0.262 Chirality : 0.041 0.140 1572 Planarity : 0.002 0.034 1659 Dihedral : 3.865 24.632 1553 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.46 (0.23), residues: 1508 helix: 2.29 (0.23), residues: 520 sheet: -1.31 (0.30), residues: 273 loop : -0.47 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.003 0.001 HIS A 197 PHE 0.018 0.001 PHE B 241 TYR 0.018 0.001 TYR R 527 ARG 0.010 0.001 ARG B 150 *********************** 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 92 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.134 Fit side-chains REVERT: B 79 LEU cc_start: 0.9073 (mp) cc_final: 0.8561 (mp) REVERT: B 188 MET cc_start: 0.8625 (mmt) cc_final: 0.8368 (mmp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1457 time to fit residues: 21.1838 Evaluate side-chains 68 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 40.0000 chunk 86 optimal weight: 50.0000 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 50.0000 chunk 148 optimal weight: 6.9990 chunk 136 optimal weight: 40.0000 chunk 118 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 91 optimal weight: 30.0000 chunk 72 optimal weight: 0.0970 chunk 93 optimal weight: 30.0000 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 615 ASN ** R 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 8866 Z= 0.391 Angle : 0.608 10.433 12250 Z= 0.341 Chirality : 0.045 0.202 1572 Planarity : 0.003 0.037 1659 Dihedral : 4.541 25.462 1553 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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: 0.01 (0.23), residues: 1508 helix: 1.80 (0.23), residues: 519 sheet: -1.64 (0.30), residues: 280 loop : -0.58 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 339 HIS 0.010 0.002 HIS B 54 PHE 0.031 0.003 PHE A 312 TYR 0.024 0.003 TYR A 327 ARG 0.007 0.001 ARG A 31 ********************** 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 75 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.938 Fit side-chains REVERT: B 188 MET cc_start: 0.8706 (mmt) cc_final: 0.8256 (mmt) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1186 time to fit residues: 15.1751 Evaluate side-chains 60 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.0570 chunk 36 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 17 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 121 optimal weight: 50.0000 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.084156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.062126 restraints weight = 34006.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062671 restraints weight = 23096.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063144 restraints weight = 17365.278| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-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: 5 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8866 Z= 0.154 Angle : 0.472 11.613 12250 Z= 0.256 Chirality : 0.042 0.178 1572 Planarity : 0.002 0.033 1659 Dihedral : 3.845 23.706 1553 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: 0.55 (0.23), residues: 1508 helix: 2.41 (0.24), residues: 514 sheet: -1.29 (0.30), residues: 290 loop : -0.40 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.015 0.001 PHE R 493 TYR 0.018 0.001 TYR R 527 ARG 0.006 0.001 ARG A 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1611.53 seconds wall clock time: 29 minutes 26.82 seconds (1766.82 seconds total)