Starting phenix.real_space_refine on Wed Sep 25 06:39:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/09_2024/7fii_31598.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/09_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_31598/09_2024/7fii_31598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/09_2024/7fii_31598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/09_2024/7fii_31598.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fii_31598/09_2024/7fii_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-5461/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: 5.89, per 1000 atoms: 0.67 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: 2.47 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: 1.17 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: 2.73 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3168 1.35 - 1.46: 2018 1.46 - 1.58: 3621 1.58 - 1.70: 0 1.70 - 1.81: 59 Bond restraints: 8866 Sorted by residual: bond pdb=" N GLU R 32 " pdb=" CA GLU R 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N CYS A 3 " pdb=" CA CYS A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLN X 5 " pdb=" CA GLN X 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N LYS Y 2 " pdb=" CA LYS Y 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 8861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 12011 1.01 - 2.03: 206 2.03 - 3.04: 17 3.04 - 4.06: 10 4.06 - 5.07: 6 Bond angle restraints: 12250 Sorted by residual: angle pdb=" N CYS R 581 " pdb=" CA CYS R 581 " pdb=" C CYS R 581 " ideal model delta sigma weight residual 114.62 111.41 3.21 1.14e+00 7.69e-01 7.91e+00 angle pdb=" C THR R 580 " pdb=" N CYS R 581 " pdb=" CA CYS R 581 " ideal model delta sigma weight residual 121.63 126.70 -5.07 1.91e+00 2.74e-01 7.05e+00 angle pdb=" CA ILE B 93 " pdb=" C ILE B 93 " pdb=" O ILE B 93 " ideal model delta sigma weight residual 120.88 119.65 1.23 6.80e-01 2.16e+00 3.26e+00 angle pdb=" CA ASP A 94 " pdb=" C ASP A 94 " pdb=" N PHE A 95 " ideal model delta sigma weight residual 114.76 116.78 -2.02 1.14e+00 7.69e-01 3.15e+00 angle pdb=" CA ILE B 93 " pdb=" C ILE B 93 " pdb=" N PRO B 94 " ideal model delta sigma weight residual 118.12 119.55 -1.43 8.10e-01 1.52e+00 3.11e+00 ... (remaining 12245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4918 16.52 - 33.04: 160 33.04 - 49.55: 34 49.55 - 66.07: 4 66.07 - 82.59: 2 Dihedral angle restraints: 5118 sinusoidal: 716 harmonic: 4402 Sorted by residual: dihedral pdb=" CB CYS X 28 " pdb=" SG CYS X 28 " pdb=" SG CYS X 82 " pdb=" CB CYS X 82 " ideal model delta sinusoidal sigma weight residual 93.00 174.74 -81.74 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS Y 38 " pdb=" SG CYS Y 38 " pdb=" SG CYS Y 90 " pdb=" CB CYS Y 90 " ideal model delta sinusoidal sigma weight residual 93.00 28.21 64.79 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CB CYS R 439 " pdb=" SG CYS R 439 " pdb=" SG CYS R 514 " pdb=" CB CYS R 514 " ideal model delta sinusoidal sigma weight residual -86.00 -126.86 40.86 1 1.00e+01 1.00e-02 2.34e+01 ... (remaining 5115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 936 0.026 - 0.052: 409 0.052 - 0.077: 108 0.077 - 0.103: 54 0.103 - 0.129: 65 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ILE R 64 " pdb=" N ILE R 64 " pdb=" C ILE R 64 " pdb=" CB ILE R 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE R 155 " pdb=" N ILE R 155 " pdb=" C ILE R 155 " pdb=" CB ILE R 155 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE R 80 " pdb=" N ILE R 80 " pdb=" C ILE R 80 " pdb=" CB ILE R 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1569 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 596 " -0.022 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO R 597 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 597 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 597 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 515 " -0.013 5.00e-02 4.00e+02 1.95e-02 6.08e-01 pdb=" N PRO R 516 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO R 516 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 516 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 612 " -0.009 5.00e-02 4.00e+02 1.39e-02 3.09e-01 pdb=" N PRO R 613 " 0.024 5.00e-02 4.00e+02 pdb=" CA PRO R 613 " -0.007 5.00e-02 4.00e+02 pdb=" CD PRO R 613 " -0.008 5.00e-02 4.00e+02 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 37 2.64 - 3.20: 7981 3.20 - 3.77: 12863 3.77 - 4.33: 14620 4.33 - 4.90: 25551 Nonbonded interactions: 61052 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" O THR B 165 " model vdw 2.073 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.138 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.361 3.040 nonbonded pdb=" OE1 GLN A 213 " pdb=" NH1 ARG B 314 " model vdw 2.388 3.120 nonbonded pdb=" O THR A 181 " pdb=" ND2 ASN B 119 " model vdw 2.409 3.120 ... (remaining 61047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.390 Find NCS groups from input model: 0.120 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: 28.800 ------------------------------------------------------------------------------- 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 : 0.969 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1394 time to fit residues: 22.1111 Evaluate side-chains 74 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.030 Fit side-chains REVERT: B 262 MET cc_start: 0.8372 (mpp) cc_final: 0.7944 (mpp) outliers start: 3 outliers final: 2 residues processed: 82 average time/residue: 0.1369 time to fit residues: 18.4049 Evaluate side-chains 68 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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: 9.9990 chunk 41 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 40.0000 chunk 146 optimal weight: 50.0000 chunk 120 optimal weight: 0.9980 chunk 134 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8866 Z= 0.191 Angle : 0.440 6.823 12250 Z= 0.249 Chirality : 0.041 0.129 1572 Planarity : 0.002 0.032 1659 Dihedral : 3.487 24.036 1553 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 1.58 (0.23), residues: 1508 helix: 2.57 (0.23), residues: 520 sheet: -0.08 (0.32), residues: 285 loop : 0.48 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS B 54 PHE 0.010 0.001 PHE R 611 TYR 0.012 0.001 TYR R 527 ARG 0.003 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 96 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.980 Fit side-chains REVERT: A 222 ILE cc_start: 0.8785 (mp) cc_final: 0.8566 (tt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1481 time to fit residues: 22.0914 Evaluate side-chains 66 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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: 0.8980 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 40.0000 chunk 64 optimal weight: 20.0000 chunk 91 optimal weight: 50.0000 chunk 136 optimal weight: 30.0000 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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: 0.7372 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8866 Z= 0.223 Angle : 0.450 7.387 12250 Z= 0.256 Chirality : 0.041 0.148 1572 Planarity : 0.002 0.032 1659 Dihedral : 3.494 26.988 1553 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.58 (0.23), residues: 518 sheet: -0.16 (0.32), residues: 277 loop : 0.35 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS B 54 PHE 0.017 0.002 PHE R 576 TYR 0.014 0.001 TYR A 327 ARG 0.003 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 95 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.981 Fit side-chains REVERT: A 222 ILE cc_start: 0.8815 (mp) cc_final: 0.8593 (tt) REVERT: B 188 MET cc_start: 0.8665 (mmt) cc_final: 0.8232 (mmp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1514 time to fit residues: 22.5748 Evaluate side-chains 63 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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: 0.9980 chunk 81 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 99 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 73 optimal weight: 0.4980 chunk 129 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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: 0.7294 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8866 Z= 0.116 Angle : 0.416 9.383 12250 Z= 0.226 Chirality : 0.040 0.147 1572 Planarity : 0.002 0.033 1659 Dihedral : 3.092 21.769 1553 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 1.72 (0.23), residues: 1508 helix: 2.87 (0.23), residues: 516 sheet: -0.09 (0.32), residues: 268 loop : 0.45 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 197 PHE 0.012 0.001 PHE A 240 TYR 0.012 0.001 TYR R 527 ARG 0.007 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 101 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.896 Fit side-chains REVERT: B 262 MET cc_start: 0.8433 (mmm) cc_final: 0.8126 (mmm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1484 time to fit residues: 23.3955 Evaluate side-chains 66 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 0.6980 chunk 129 optimal weight: 30.0000 chunk 28 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 chunk 35 optimal weight: 30.0000 chunk 144 optimal weight: 50.0000 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 47 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- 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: 0.7476 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 8866 Z= 0.406 Angle : 0.600 7.808 12250 Z= 0.340 Chirality : 0.044 0.161 1572 Planarity : 0.003 0.035 1659 Dihedral : 4.243 27.544 1553 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.81 (0.23), residues: 1508 helix: 2.08 (0.24), residues: 518 sheet: -0.75 (0.31), residues: 284 loop : 0.02 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.010 0.002 HIS B 54 PHE 0.034 0.003 PHE A 240 TYR 0.024 0.003 TYR A 327 ARG 0.006 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 86 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.036 Fit side-chains REVERT: B 188 MET cc_start: 0.8559 (mmt) cc_final: 0.8112 (mmt) REVERT: B 262 MET cc_start: 0.8411 (mmm) cc_final: 0.8195 (mmm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1212 time to fit residues: 18.0107 Evaluate side-chains 63 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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: 20.0000 chunk 16 optimal weight: 40.0000 chunk 82 optimal weight: 50.0000 chunk 105 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 121 optimal weight: 40.0000 chunk 80 optimal weight: 20.0000 chunk 143 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- 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: 0.7485 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8866 Z= 0.349 Angle : 0.560 9.887 12250 Z= 0.313 Chirality : 0.044 0.172 1572 Planarity : 0.003 0.034 1659 Dihedral : 4.274 26.830 1553 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.23), residues: 1508 helix: 2.00 (0.23), residues: 519 sheet: -1.12 (0.29), residues: 297 loop : -0.22 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.002 HIS B 54 PHE 0.024 0.002 PHE A 240 TYR 0.025 0.002 TYR B 105 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 : 1.038 Fit side-chains REVERT: B 79 LEU cc_start: 0.9114 (mp) cc_final: 0.8479 (mp) REVERT: B 105 TYR cc_start: 0.7051 (t80) cc_final: 0.6722 (t80) REVERT: B 188 MET cc_start: 0.8664 (mmt) cc_final: 0.8161 (mmt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1467 time to fit residues: 20.3161 Evaluate side-chains 65 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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: 40.0000 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 91 optimal weight: 40.0000 chunk 97 optimal weight: 30.0000 chunk 71 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS R 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 8866 Z= 0.445 Angle : 0.631 10.175 12250 Z= 0.357 Chirality : 0.046 0.176 1572 Planarity : 0.003 0.035 1659 Dihedral : 4.723 27.746 1553 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.02 (0.22), residues: 1508 helix: 1.52 (0.23), residues: 524 sheet: -1.39 (0.28), residues: 302 loop : -0.41 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 82 HIS 0.013 0.002 HIS B 54 PHE 0.028 0.003 PHE A 240 TYR 0.024 0.003 TYR B 105 ARG 0.006 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 82 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.063 Fit side-chains REVERT: B 105 TYR cc_start: 0.7323 (t80) cc_final: 0.6971 (t80) REVERT: B 188 MET cc_start: 0.8592 (mmt) cc_final: 0.8144 (mmt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1316 time to fit residues: 17.9619 Evaluate side-chains 59 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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: 20.0000 chunk 137 optimal weight: 50.0000 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 80 optimal weight: 50.0000 chunk 58 optimal weight: 0.0970 chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- 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: 0.7431 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8866 Z= 0.177 Angle : 0.482 11.110 12250 Z= 0.263 Chirality : 0.042 0.188 1572 Planarity : 0.002 0.035 1659 Dihedral : 3.950 27.134 1553 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.23), residues: 1508 helix: 2.37 (0.23), residues: 514 sheet: -1.33 (0.29), residues: 301 loop : -0.16 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 169 HIS 0.006 0.001 HIS A 197 PHE 0.019 0.002 PHE B 241 TYR 0.014 0.001 TYR R 527 ARG 0.004 0.001 ARG A 208 *********************** 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 90 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.014 Fit side-chains REVERT: R 398 MET cc_start: 0.7654 (mmp) cc_final: 0.7324 (tpp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1231 time to fit residues: 19.1696 Evaluate side-chains 64 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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: 30.0000 chunk 86 optimal weight: 50.0000 chunk 67 optimal weight: 5.9990 chunk 98 optimal weight: 50.0000 chunk 148 optimal weight: 30.0000 chunk 136 optimal weight: 40.0000 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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: 0.7532 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 8866 Z= 0.420 Angle : 0.614 10.276 12250 Z= 0.346 Chirality : 0.045 0.180 1572 Planarity : 0.003 0.036 1659 Dihedral : 4.538 25.146 1553 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % 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: 0.15 (0.23), residues: 1508 helix: 1.80 (0.23), residues: 519 sheet: -1.44 (0.29), residues: 291 loop : -0.42 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 169 HIS 0.011 0.002 HIS A 197 PHE 0.033 0.003 PHE A 240 TYR 0.023 0.003 TYR A 327 ARG 0.004 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 81 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.067 Fit side-chains REVERT: B 188 MET cc_start: 0.8558 (mmt) cc_final: 0.8067 (mmt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1231 time to fit residues: 16.9925 Evaluate side-chains 58 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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: 0.0030 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 17 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 121 optimal weight: 50.0000 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.084905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.062961 restraints weight = 33358.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063559 restraints weight = 22422.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063716 restraints weight = 16541.854| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 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 = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8866 Z= 0.153 Angle : 0.472 11.303 12250 Z= 0.256 Chirality : 0.041 0.179 1572 Planarity : 0.002 0.035 1659 Dihedral : 3.793 24.408 1553 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.23), residues: 1508 helix: 2.53 (0.24), residues: 508 sheet: -1.41 (0.29), residues: 285 loop : -0.12 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 169 HIS 0.005 0.001 HIS A 197 PHE 0.011 0.001 PHE A 189 TYR 0.013 0.001 TYR R 527 ARG 0.005 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.99 seconds wall clock time: 29 minutes 25.35 seconds (1765.35 seconds total)