Starting phenix.real_space_refine on Fri Jan 17 16:14:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x52_38059/01_2025/8x52_38059.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x52_38059/01_2025/8x52_38059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x52_38059/01_2025/8x52_38059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x52_38059/01_2025/8x52_38059.map" model { file = "/net/cci-nas-00/data/ceres_data/8x52_38059/01_2025/8x52_38059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x52_38059/01_2025/8x52_38059.cif" } resolution = 2.9 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= -0.001 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 43 5.16 5 C 7142 2.51 5 N 1727 2.21 5 O 1993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10907 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 145 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "A" Number of atoms: 5233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5233 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2424 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1872 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 814 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'CLR': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 7.25, per 1000 atoms: 0.66 Number of scatterers: 10907 At special positions: 0 Unit cell: (109.79, 95.5173, 131.748, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 2 15.00 O 1993 8.00 N 1727 7.00 C 7142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS A 242 " distance=1.47 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " 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 Links applied BETA1-3 " BMA G 3 " - " BMA G 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " NAG-ASN " NAG A 801 " - " ASN A 387 " " NAG A 802 " - " ASN A 464 " " NAG A 803 " - " ASN A 506 " " NAG A 804 " - " ASN A 264 " " NAG A 805 " - " ASN A 187 " " NAG A 806 " - " ASN A 580 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 55 " " NAG H 1 " - " ASN A 435 " " NAG I 1 " - " ASN A 573 " " NAG J 1 " - " ASN A 530 " " NAG K 1 " - " ASN A 562 " Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.5 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 58.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'E' and resid 30 through 37 removed outlier: 3.614A pdb=" N LEU E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 42 removed outlier: 3.536A pdb=" N ILE E 41 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 79 through 87 removed outlier: 4.052A pdb=" N GLN A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.948A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.597A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.888A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.513A pdb=" N SER A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.767A pdb=" N LYS A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.072A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.555A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.699A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.724A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 589 through 592 Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.751A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.775A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.898A pdb=" N VAL B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 124 through 156 Processing helix chain 'B' and resid 158 through 175 removed outlier: 4.032A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.919A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.969A pdb=" N PHE B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.977A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 450 removed outlier: 4.187A pdb=" N PHE B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.626A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 28 through 61 removed outlier: 3.903A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 103 removed outlier: 3.739A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 3.534A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.768A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.872A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 191 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.661A pdb=" N ALA C 212 " --> pdb=" O TRP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.790A pdb=" N GLY D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.591A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 81 removed outlier: 4.129A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing sheet with id=AA1, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.765A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET A 95 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 72 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 97 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS A 74 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLU A 99 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VAL A 76 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 94 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA4, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.550A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 275 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL A 363 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 277 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 365 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA A 279 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 579 removed outlier: 3.509A pdb=" N VAL A 579 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.551A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1668 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: 3.36 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 71 1.23 - 1.37: 3543 1.37 - 1.52: 4934 1.52 - 1.67: 2566 1.67 - 1.81: 66 Bond restraints: 11180 Sorted by residual: bond pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 1.467 1.685 -0.218 1.17e-02 7.31e+03 3.48e+02 bond pdb=" C GLY B 384 " pdb=" O GLY B 384 " ideal model delta sigma weight residual 1.236 1.090 0.146 1.08e-02 8.57e+03 1.82e+02 bond pdb=" C LEU B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 1.335 1.501 -0.166 1.38e-02 5.25e+03 1.45e+02 bond pdb=" C PRO B 433 " pdb=" O PRO B 433 " ideal model delta sigma weight residual 1.233 1.080 0.153 1.39e-02 5.18e+03 1.22e+02 bond pdb=" C LEU B 435 " pdb=" O LEU B 435 " ideal model delta sigma weight residual 1.244 1.150 0.094 9.10e-03 1.21e+04 1.07e+02 ... (remaining 11175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 15170 5.73 - 11.46: 62 11.46 - 17.18: 10 17.18 - 22.91: 0 22.91 - 28.64: 1 Bond angle restraints: 15243 Sorted by residual: angle pdb=" N GLY C 233 " pdb=" CA GLY C 233 " pdb=" C GLY C 233 " ideal model delta sigma weight residual 115.43 144.07 -28.64 1.41e+00 5.03e-01 4.13e+02 angle pdb=" C LEU B 432 " pdb=" N PRO B 433 " pdb=" CA PRO B 433 " ideal model delta sigma weight residual 119.93 137.02 -17.09 1.07e+00 8.73e-01 2.55e+02 angle pdb=" CA LEU B 435 " pdb=" C LEU B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 120.58 130.94 -10.36 7.40e-01 1.83e+00 1.96e+02 angle pdb=" C LEU B 435 " pdb=" N PRO B 436 " pdb=" CA PRO B 436 " ideal model delta sigma weight residual 119.24 131.85 -12.61 1.04e+00 9.25e-01 1.47e+02 angle pdb=" O LEU B 432 " pdb=" C LEU B 432 " pdb=" N PRO B 433 " ideal model delta sigma weight residual 121.72 111.32 10.40 9.80e-01 1.04e+00 1.13e+02 ... (remaining 15238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 6630 23.49 - 46.98: 207 46.98 - 70.46: 43 70.46 - 93.95: 21 93.95 - 117.44: 18 Dihedral angle restraints: 6919 sinusoidal: 3033 harmonic: 3886 Sorted by residual: dihedral pdb=" CB CYS A 586 " pdb=" SG CYS A 586 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual -86.00 -164.69 78.69 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" C PHE B 386 " pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" CB PHE B 386 " ideal model delta harmonic sigma weight residual -122.60 -104.19 -18.41 0 2.50e+00 1.60e-01 5.42e+01 dihedral pdb=" CB CYS E 28 " pdb=" SG CYS E 28 " pdb=" SG CYS A 242 " pdb=" CB CYS A 242 " ideal model delta sinusoidal sigma weight residual 93.00 30.42 62.58 1 1.00e+01 1.00e-02 5.18e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1782 0.146 - 0.292: 36 0.292 - 0.438: 10 0.438 - 0.584: 1 0.584 - 0.730: 1 Chirality restraints: 1830 Sorted by residual: chirality pdb=" CA PRO B 433 " pdb=" N PRO B 433 " pdb=" C PRO B 433 " pdb=" CB PRO B 433 " both_signs ideal model delta sigma weight residual False 2.72 3.45 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 1827 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " 0.117 2.00e-02 2.50e+03 1.19e-01 1.78e+02 pdb=" CG ASN A 573 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " -0.187 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " -0.013 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 114 " 0.021 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ILE B 114 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE B 114 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR B 115 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 284 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C PRO B 284 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO B 284 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 285 " 0.022 2.00e-02 2.50e+03 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 3 2.26 - 2.92: 4391 2.92 - 3.58: 15318 3.58 - 4.24: 25252 4.24 - 4.90: 42436 Nonbonded interactions: 87400 Sorted by model distance: nonbonded pdb=" OD1 ASN A 573 " pdb=" C1 NAG I 1 " model vdw 1.598 2.776 nonbonded pdb=" OH TYR B 389 " pdb=" O ALA B 434 " model vdw 2.168 3.040 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.263 3.040 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.297 3.040 ... (remaining 87395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.330 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 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 : 0.009 0.218 11180 Z= 0.558 Angle : 1.131 28.640 15243 Z= 0.685 Chirality : 0.066 0.730 1830 Planarity : 0.007 0.071 1845 Dihedral : 14.341 117.440 4400 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.69 % Favored : 95.16 % Rotamer: Outliers : 0.88 % Allowed : 2.98 % Favored : 96.14 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % 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: -3.49 (0.18), residues: 1322 helix: -1.90 (0.15), residues: 722 sheet: -1.54 (0.47), residues: 114 loop : -2.97 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP C 227 HIS 0.024 0.003 HIS C 197 PHE 0.040 0.003 PHE B 386 TYR 0.035 0.003 TYR A 565 ARG 0.009 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 267 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.6147 (m110) cc_final: 0.5830 (m110) REVERT: A 37 GLU cc_start: 0.6912 (pt0) cc_final: 0.6573 (pt0) REVERT: A 58 HIS cc_start: 0.6969 (m90) cc_final: 0.6035 (m90) REVERT: A 78 LYS cc_start: 0.6766 (ptpt) cc_final: 0.6278 (pttm) REVERT: A 81 ASP cc_start: 0.5412 (m-30) cc_final: 0.4677 (m-30) REVERT: A 143 ASP cc_start: 0.6268 (t0) cc_final: 0.6011 (t70) REVERT: A 201 LEU cc_start: 0.7606 (mt) cc_final: 0.7318 (mm) REVERT: A 224 VAL cc_start: 0.7972 (m) cc_final: 0.7630 (t) REVERT: A 237 GLN cc_start: 0.6411 (mm-40) cc_final: 0.5699 (tm-30) REVERT: A 357 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7748 (pm20) REVERT: A 374 LEU cc_start: 0.7211 (mt) cc_final: 0.6950 (mp) REVERT: A 391 ARG cc_start: 0.6665 (ttp-110) cc_final: 0.6204 (ttm110) REVERT: A 392 ASN cc_start: 0.7428 (m-40) cc_final: 0.7098 (m-40) REVERT: A 474 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6715 (mp0) REVERT: A 478 ASN cc_start: 0.7820 (m-40) cc_final: 0.7455 (m-40) REVERT: A 500 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7190 (tt0) REVERT: A 509 ASP cc_start: 0.7397 (m-30) cc_final: 0.6425 (p0) REVERT: A 540 GLN cc_start: 0.7852 (tt0) cc_final: 0.7600 (tp40) REVERT: A 543 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6667 (mtm110) REVERT: A 565 TYR cc_start: 0.7732 (m-80) cc_final: 0.7311 (m-80) REVERT: A 666 LYS cc_start: 0.5949 (tptt) cc_final: 0.5542 (ttpt) REVERT: B 80 LYS cc_start: 0.6672 (tptt) cc_final: 0.6377 (tptt) REVERT: B 130 LEU cc_start: 0.7391 (tp) cc_final: 0.7126 (mm) REVERT: B 155 LYS cc_start: 0.7243 (tptt) cc_final: 0.7018 (tttm) REVERT: B 163 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7410 (m-70) REVERT: B 187 LYS cc_start: 0.6847 (mttp) cc_final: 0.6624 (mtmp) REVERT: B 380 LYS cc_start: 0.7257 (mttm) cc_final: 0.6939 (mptt) REVERT: C 52 VAL cc_start: 0.7687 (t) cc_final: 0.7318 (m) REVERT: C 56 LEU cc_start: 0.8019 (mt) cc_final: 0.7763 (mt) REVERT: C 119 TYR cc_start: 0.7007 (t80) cc_final: 0.6754 (t80) REVERT: C 140 ASP cc_start: 0.7438 (m-30) cc_final: 0.7043 (m-30) REVERT: C 146 VAL cc_start: 0.7406 (p) cc_final: 0.7086 (m) REVERT: D 59 ARG cc_start: 0.5719 (ttm170) cc_final: 0.5189 (tmt170) REVERT: D 84 ARG cc_start: 0.6642 (mtt90) cc_final: 0.6361 (mtm180) REVERT: D 91 TYR cc_start: 0.6352 (m-80) cc_final: 0.6149 (m-10) outliers start: 10 outliers final: 7 residues processed: 271 average time/residue: 1.0797 time to fit residues: 318.8513 Evaluate side-chains 168 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain D residue 69 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 194 GLN A 355 GLN A 358 ASN A 385 GLN A 393 GLN A 454 GLN A 531 ASN B 214 HIS B 405 ASN B 454 GLN B 463 HIS C 58 HIS C 68 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.152707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122921 restraints weight = 14419.891| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.29 r_work: 0.3379 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11180 Z= 0.233 Angle : 0.665 9.485 15243 Z= 0.329 Chirality : 0.045 0.403 1830 Planarity : 0.005 0.050 1845 Dihedral : 12.453 104.884 2084 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.24 % Allowed : 10.96 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.22), residues: 1322 helix: 0.20 (0.19), residues: 721 sheet: -1.11 (0.49), residues: 109 loop : -2.30 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 209 HIS 0.011 0.001 HIS C 197 PHE 0.037 0.002 PHE A 302 TYR 0.028 0.002 TYR A 645 ARG 0.008 0.001 ARG A 520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.6945 (tp) REVERT: A 58 HIS cc_start: 0.8100 (m90) cc_final: 0.7677 (m90) REVERT: A 81 ASP cc_start: 0.6338 (m-30) cc_final: 0.6040 (m-30) REVERT: A 237 GLN cc_start: 0.6966 (mm-40) cc_final: 0.6525 (tm-30) REVERT: A 391 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7294 (ttm110) REVERT: A 392 ASN cc_start: 0.8118 (m-40) cc_final: 0.7773 (m-40) REVERT: A 509 ASP cc_start: 0.7434 (m-30) cc_final: 0.6637 (p0) REVERT: A 543 ARG cc_start: 0.7869 (mtm180) cc_final: 0.7585 (mtm110) REVERT: A 617 LEU cc_start: 0.8132 (mp) cc_final: 0.7795 (mm) REVERT: B 80 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7407 (tptt) REVERT: B 128 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7212 (ttp-170) REVERT: B 130 LEU cc_start: 0.8061 (tp) cc_final: 0.7860 (mm) REVERT: B 154 TYR cc_start: 0.8428 (t80) cc_final: 0.8139 (t80) REVERT: B 163 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7587 (m-70) REVERT: B 165 TRP cc_start: 0.8405 (t60) cc_final: 0.8110 (t60) REVERT: B 169 SER cc_start: 0.8604 (t) cc_final: 0.8090 (p) REVERT: B 184 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6870 (mm-30) REVERT: B 380 LYS cc_start: 0.7234 (mttm) cc_final: 0.6847 (mptt) REVERT: B 463 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8428 (m90) REVERT: C 140 ASP cc_start: 0.8277 (m-30) cc_final: 0.7898 (m-30) REVERT: D 59 ARG cc_start: 0.6627 (ttm170) cc_final: 0.6064 (tmt170) outliers start: 37 outliers final: 17 residues processed: 202 average time/residue: 1.0294 time to fit residues: 228.9355 Evaluate side-chains 157 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 0.0270 chunk 94 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.0170 chunk 47 optimal weight: 0.6980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN A 531 ASN A 596 ASN B 463 HIS C 58 HIS D 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119307 restraints weight = 14630.309| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.29 r_work: 0.3333 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11180 Z= 0.183 Angle : 0.612 9.781 15243 Z= 0.296 Chirality : 0.043 0.382 1830 Planarity : 0.004 0.043 1845 Dihedral : 10.630 111.011 2078 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.43 % Rotamer: Outliers : 3.86 % Allowed : 14.02 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.23), residues: 1322 helix: 0.87 (0.19), residues: 732 sheet: -1.04 (0.46), residues: 120 loop : -1.96 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 209 HIS 0.012 0.001 HIS B 463 PHE 0.034 0.002 PHE A 302 TYR 0.016 0.001 TYR A 569 ARG 0.006 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.6882 (tp) REVERT: A 58 HIS cc_start: 0.8373 (m90) cc_final: 0.7987 (m90) REVERT: A 249 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7884 (t0) REVERT: A 391 ARG cc_start: 0.7624 (ttp-110) cc_final: 0.7389 (ttm110) REVERT: A 392 ASN cc_start: 0.8070 (m-40) cc_final: 0.7735 (m-40) REVERT: A 543 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7552 (mtm110) REVERT: A 598 ASP cc_start: 0.7620 (p0) cc_final: 0.7145 (p0) REVERT: A 617 LEU cc_start: 0.8185 (mp) cc_final: 0.7896 (mm) REVERT: A 624 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8486 (m) REVERT: B 128 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7150 (ttp-170) REVERT: B 130 LEU cc_start: 0.8063 (tp) cc_final: 0.7816 (mm) REVERT: B 154 TYR cc_start: 0.8327 (t80) cc_final: 0.8112 (t80) REVERT: B 163 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7547 (m-70) REVERT: B 169 SER cc_start: 0.8827 (t) cc_final: 0.8329 (p) REVERT: B 177 PHE cc_start: 0.8360 (m-80) cc_final: 0.8149 (m-80) REVERT: B 380 LYS cc_start: 0.7556 (mttm) cc_final: 0.7116 (mptt) REVERT: C 31 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7719 (mtt180) REVERT: C 62 ARG cc_start: 0.6568 (mmt90) cc_final: 0.5674 (ttp80) REVERT: C 140 ASP cc_start: 0.8377 (m-30) cc_final: 0.8161 (m-30) REVERT: C 167 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7908 (mp) REVERT: C 186 ARG cc_start: 0.8103 (ptp-170) cc_final: 0.7713 (ptp-170) REVERT: C 206 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8011 (mt) REVERT: D 59 ARG cc_start: 0.6881 (ttm170) cc_final: 0.6206 (tmt170) REVERT: D 84 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6934 (mtm180) outliers start: 44 outliers final: 16 residues processed: 170 average time/residue: 0.9966 time to fit residues: 187.1101 Evaluate side-chains 149 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 18 TYR Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 142 ASN A 255 ASN A 444 HIS A 596 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101889 restraints weight = 14482.714| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.26 r_work: 0.3093 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 11180 Z= 0.342 Angle : 0.685 11.723 15243 Z= 0.337 Chirality : 0.046 0.300 1830 Planarity : 0.005 0.051 1845 Dihedral : 9.807 108.323 2074 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 5.35 % Allowed : 14.37 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.23), residues: 1322 helix: 0.93 (0.19), residues: 738 sheet: -0.99 (0.46), residues: 124 loop : -1.96 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 209 HIS 0.008 0.002 HIS C 197 PHE 0.033 0.003 PHE A 302 TYR 0.026 0.002 TYR A 499 ARG 0.022 0.001 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 146 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 118 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 391 ARG cc_start: 0.7719 (ttp-110) cc_final: 0.7259 (ttm110) REVERT: A 392 ASN cc_start: 0.8059 (m-40) cc_final: 0.7610 (m-40) REVERT: A 543 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7494 (mtm110) REVERT: A 585 GLN cc_start: 0.7734 (mt0) cc_final: 0.7305 (mt0) REVERT: A 617 LEU cc_start: 0.8429 (mp) cc_final: 0.8225 (mm) REVERT: A 624 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8804 (m) REVERT: A 655 ASP cc_start: 0.6538 (t0) cc_final: 0.6079 (t70) REVERT: A 666 LYS cc_start: 0.7374 (tptt) cc_final: 0.6818 (ttpt) REVERT: A 677 PHE cc_start: 0.8299 (m-80) cc_final: 0.8012 (m-10) REVERT: B 80 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7450 (tppt) REVERT: B 128 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7061 (ttp-170) REVERT: B 130 LEU cc_start: 0.8070 (tp) cc_final: 0.7844 (mm) REVERT: B 163 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7567 (m-70) REVERT: B 177 PHE cc_start: 0.8418 (m-80) cc_final: 0.8172 (m-80) REVERT: B 184 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7399 (mm-30) REVERT: B 253 ILE cc_start: 0.8382 (tt) cc_final: 0.8155 (tt) REVERT: B 429 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8285 (mtmm) REVERT: C 62 ARG cc_start: 0.6726 (mmt90) cc_final: 0.6010 (ttp80) REVERT: C 206 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8223 (mt) REVERT: C 236 LEU cc_start: 0.8069 (mm) cc_final: 0.7747 (tp) REVERT: D 59 ARG cc_start: 0.7574 (ttm170) cc_final: 0.6782 (tmt170) REVERT: D 84 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7048 (mtm180) outliers start: 61 outliers final: 19 residues processed: 191 average time/residue: 1.0262 time to fit residues: 215.4650 Evaluate side-chains 145 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 80 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 0.0570 chunk 40 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 16 optimal weight: 0.0000 chunk 99 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 222 HIS A 393 GLN A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104302 restraints weight = 14439.465| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.27 r_work: 0.3129 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11180 Z= 0.178 Angle : 0.603 11.748 15243 Z= 0.290 Chirality : 0.043 0.283 1830 Planarity : 0.004 0.038 1845 Dihedral : 9.211 98.318 2073 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 3.51 % Allowed : 17.97 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.24), residues: 1322 helix: 1.37 (0.20), residues: 731 sheet: -0.94 (0.46), residues: 123 loop : -1.70 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.031 0.001 PHE A 302 TYR 0.021 0.001 TYR A 499 ARG 0.006 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 118 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 231 MET cc_start: 0.8293 (mmm) cc_final: 0.8071 (mmp) REVERT: A 253 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8388 (t0) REVERT: A 364 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: A 391 ARG cc_start: 0.7701 (ttp-110) cc_final: 0.7497 (ttm110) REVERT: A 392 ASN cc_start: 0.8069 (m-40) cc_final: 0.7642 (m-40) REVERT: A 436 ILE cc_start: 0.8967 (pt) cc_final: 0.8599 (mt) REVERT: A 482 ASP cc_start: 0.7704 (m-30) cc_final: 0.7335 (m-30) REVERT: A 543 ARG cc_start: 0.7783 (mtm180) cc_final: 0.7437 (mtm110) REVERT: A 582 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7105 (m) REVERT: A 624 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8689 (m) REVERT: A 655 ASP cc_start: 0.6335 (t0) cc_final: 0.5861 (t70) REVERT: A 677 PHE cc_start: 0.8267 (m-80) cc_final: 0.7970 (m-10) REVERT: B 128 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7008 (ttp-170) REVERT: B 130 LEU cc_start: 0.8091 (tp) cc_final: 0.7860 (mm) REVERT: B 163 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7498 (m-70) REVERT: B 184 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7271 (mm-30) REVERT: B 253 ILE cc_start: 0.8341 (tt) cc_final: 0.8097 (tt) REVERT: B 457 MET cc_start: 0.9187 (tpp) cc_final: 0.8929 (mmt) REVERT: C 62 ARG cc_start: 0.6558 (mmt90) cc_final: 0.5953 (ttp80) REVERT: C 186 ARG cc_start: 0.8243 (ptp-170) cc_final: 0.7949 (ptp-170) REVERT: C 206 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8112 (mt) REVERT: C 236 LEU cc_start: 0.8043 (mm) cc_final: 0.7738 (tp) REVERT: D 59 ARG cc_start: 0.7584 (ttm170) cc_final: 0.6735 (tmt170) REVERT: D 84 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7141 (mtm180) outliers start: 40 outliers final: 14 residues processed: 165 average time/residue: 0.9426 time to fit residues: 172.2168 Evaluate side-chains 141 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.0970 chunk 68 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 124 optimal weight: 0.0770 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 255 ASN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104479 restraints weight = 14533.164| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.27 r_work: 0.3131 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11180 Z= 0.184 Angle : 0.587 11.318 15243 Z= 0.282 Chirality : 0.042 0.283 1830 Planarity : 0.004 0.038 1845 Dihedral : 8.665 82.016 2073 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 3.86 % Allowed : 18.76 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.24), residues: 1322 helix: 1.58 (0.20), residues: 731 sheet: -1.04 (0.45), residues: 123 loop : -1.66 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 84 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.018 0.001 TYR A 499 ARG 0.007 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 118 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 249 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7836 (p0) REVERT: A 253 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8427 (t0) REVERT: A 364 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: A 391 ARG cc_start: 0.7680 (ttp-110) cc_final: 0.7294 (ttm110) REVERT: A 392 ASN cc_start: 0.8036 (m-40) cc_final: 0.7625 (m-40) REVERT: A 482 ASP cc_start: 0.7757 (m-30) cc_final: 0.7446 (m-30) REVERT: A 540 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8004 (tp40) REVERT: A 543 ARG cc_start: 0.7770 (mtm180) cc_final: 0.7427 (mtm110) REVERT: A 624 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8632 (m) REVERT: A 655 ASP cc_start: 0.6446 (t0) cc_final: 0.5955 (t70) REVERT: A 677 PHE cc_start: 0.8284 (m-80) cc_final: 0.7913 (m-10) REVERT: B 128 ARG cc_start: 0.7568 (mtp180) cc_final: 0.6990 (ttp-170) REVERT: B 130 LEU cc_start: 0.8036 (tp) cc_final: 0.7800 (mm) REVERT: B 253 ILE cc_start: 0.8157 (tt) cc_final: 0.7912 (tt) REVERT: B 457 MET cc_start: 0.9130 (tpp) cc_final: 0.8924 (mmt) REVERT: C 55 ILE cc_start: 0.7457 (mt) cc_final: 0.7172 (mt) REVERT: C 62 ARG cc_start: 0.6619 (mmt90) cc_final: 0.5967 (ttp80) REVERT: D 59 ARG cc_start: 0.7602 (ttm170) cc_final: 0.6742 (mmt180) REVERT: D 84 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7136 (mtm180) outliers start: 44 outliers final: 18 residues processed: 167 average time/residue: 0.9294 time to fit residues: 172.7200 Evaluate side-chains 145 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 121 optimal weight: 0.0020 chunk 45 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 393 GLN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104901 restraints weight = 14770.454| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.26 r_work: 0.3127 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11180 Z= 0.183 Angle : 0.578 11.171 15243 Z= 0.279 Chirality : 0.042 0.278 1830 Planarity : 0.004 0.040 1845 Dihedral : 7.959 71.852 2071 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 3.24 % Allowed : 19.98 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.24), residues: 1322 helix: 1.69 (0.20), residues: 730 sheet: -1.01 (0.45), residues: 123 loop : -1.58 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.017 0.001 TYR A 499 ARG 0.005 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8033 (tp) REVERT: A 118 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8342 (mp) REVERT: A 249 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7824 (p0) REVERT: A 253 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8339 (t0) REVERT: A 259 MET cc_start: 0.9339 (tpt) cc_final: 0.9112 (tpp) REVERT: A 364 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: A 391 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7323 (ttm110) REVERT: A 392 ASN cc_start: 0.8080 (m-40) cc_final: 0.7665 (m-40) REVERT: A 482 ASP cc_start: 0.7824 (m-30) cc_final: 0.7580 (m-30) REVERT: A 543 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7574 (mtm-85) REVERT: A 624 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8675 (m) REVERT: A 655 ASP cc_start: 0.6401 (t0) cc_final: 0.5928 (t70) REVERT: B 130 LEU cc_start: 0.8081 (tp) cc_final: 0.7845 (mm) REVERT: B 147 THR cc_start: 0.6939 (m) cc_final: 0.6701 (m) REVERT: B 165 TRP cc_start: 0.8532 (t60) cc_final: 0.8027 (t60) REVERT: B 253 ILE cc_start: 0.8194 (tt) cc_final: 0.7973 (tt) REVERT: B 256 TYR cc_start: 0.7446 (t80) cc_final: 0.6998 (t80) REVERT: C 55 ILE cc_start: 0.7499 (mt) cc_final: 0.7193 (mt) REVERT: C 62 ARG cc_start: 0.6688 (mmt90) cc_final: 0.6121 (ttp80) REVERT: D 59 ARG cc_start: 0.7666 (ttm170) cc_final: 0.6741 (mmt180) REVERT: D 84 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7115 (mtm180) outliers start: 37 outliers final: 16 residues processed: 163 average time/residue: 1.0041 time to fit residues: 180.9748 Evaluate side-chains 147 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 393 GLN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102606 restraints weight = 14422.689| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.27 r_work: 0.3085 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11180 Z= 0.235 Angle : 0.602 11.236 15243 Z= 0.290 Chirality : 0.043 0.270 1830 Planarity : 0.004 0.056 1845 Dihedral : 7.672 71.482 2071 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 3.42 % Allowed : 19.81 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1322 helix: 1.68 (0.20), residues: 727 sheet: -0.95 (0.45), residues: 121 loop : -1.53 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 244 HIS 0.006 0.001 HIS C 197 PHE 0.030 0.002 PHE A 302 TYR 0.024 0.001 TYR B 115 ARG 0.004 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8060 (tp) REVERT: A 37 GLU cc_start: 0.8527 (pt0) cc_final: 0.8250 (pt0) REVERT: A 118 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 237 GLN cc_start: 0.7237 (tp40) cc_final: 0.6811 (mm110) REVERT: A 249 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7809 (p0) REVERT: A 253 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8487 (t0) REVERT: A 364 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: A 391 ARG cc_start: 0.7649 (ttp-110) cc_final: 0.7252 (ttm110) REVERT: A 392 ASN cc_start: 0.7962 (m-40) cc_final: 0.7593 (m-40) REVERT: A 482 ASP cc_start: 0.7843 (m-30) cc_final: 0.7602 (m-30) REVERT: A 543 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7526 (mtm-85) REVERT: A 624 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8771 (m) REVERT: A 655 ASP cc_start: 0.6684 (t0) cc_final: 0.6183 (t70) REVERT: B 130 LEU cc_start: 0.8038 (tp) cc_final: 0.7818 (mm) REVERT: B 147 THR cc_start: 0.7007 (m) cc_final: 0.6587 (m) REVERT: B 165 TRP cc_start: 0.8554 (t60) cc_final: 0.8075 (t60) REVERT: B 253 ILE cc_start: 0.8302 (tt) cc_final: 0.8081 (tt) REVERT: C 55 ILE cc_start: 0.7520 (mt) cc_final: 0.7249 (mt) REVERT: C 62 ARG cc_start: 0.6738 (mmt90) cc_final: 0.6171 (ttp80) REVERT: D 59 ARG cc_start: 0.7583 (ttm170) cc_final: 0.6776 (mmt180) REVERT: D 84 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7326 (mtm180) outliers start: 39 outliers final: 20 residues processed: 165 average time/residue: 1.0966 time to fit residues: 198.0799 Evaluate side-chains 156 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 89 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 393 GLN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.133675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101266 restraints weight = 14529.015| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.32 r_work: 0.3092 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11180 Z= 0.245 Angle : 0.607 11.121 15243 Z= 0.294 Chirality : 0.043 0.269 1830 Planarity : 0.004 0.066 1845 Dihedral : 7.356 63.885 2071 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 3.51 % Allowed : 20.25 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1322 helix: 1.67 (0.20), residues: 728 sheet: -0.94 (0.45), residues: 121 loop : -1.51 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 244 HIS 0.005 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.022 0.001 TYR B 115 ARG 0.005 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8235 (tp) REVERT: A 37 GLU cc_start: 0.8653 (pt0) cc_final: 0.8429 (pt0) REVERT: A 237 GLN cc_start: 0.7260 (tp40) cc_final: 0.6850 (mm110) REVERT: A 253 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8280 (t0) REVERT: A 259 MET cc_start: 0.9440 (tpt) cc_final: 0.9206 (tpp) REVERT: A 364 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: A 391 ARG cc_start: 0.7662 (ttp-110) cc_final: 0.7389 (ttm110) REVERT: A 392 ASN cc_start: 0.8040 (m-40) cc_final: 0.7562 (m110) REVERT: A 543 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7741 (mtm-85) REVERT: A 624 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8876 (m) REVERT: A 655 ASP cc_start: 0.6663 (t0) cc_final: 0.6290 (t70) REVERT: B 147 THR cc_start: 0.7020 (m) cc_final: 0.6820 (m) REVERT: B 165 TRP cc_start: 0.8581 (t60) cc_final: 0.8026 (t60) REVERT: B 253 ILE cc_start: 0.8477 (tt) cc_final: 0.8253 (tt) REVERT: B 256 TYR cc_start: 0.7531 (t80) cc_final: 0.7021 (t80) REVERT: C 62 ARG cc_start: 0.6869 (mmt90) cc_final: 0.6334 (ttp80) REVERT: C 186 ARG cc_start: 0.8450 (ptm-80) cc_final: 0.8181 (ptp-170) REVERT: D 59 ARG cc_start: 0.7731 (ttm170) cc_final: 0.6912 (mmt180) REVERT: D 84 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7447 (mtm180) outliers start: 40 outliers final: 21 residues processed: 158 average time/residue: 1.0717 time to fit residues: 185.7390 Evaluate side-chains 149 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 119 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 0.0020 chunk 122 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103152 restraints weight = 14388.696| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.31 r_work: 0.3119 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11180 Z= 0.186 Angle : 0.588 10.856 15243 Z= 0.283 Chirality : 0.042 0.269 1830 Planarity : 0.004 0.061 1845 Dihedral : 6.958 56.519 2069 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.54 % Allowed : 21.38 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.24), residues: 1322 helix: 1.74 (0.20), residues: 728 sheet: -1.00 (0.46), residues: 118 loop : -1.51 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 36 HIS 0.005 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.027 0.001 TYR B 115 ARG 0.011 0.001 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8323 (tp) REVERT: A 37 GLU cc_start: 0.8633 (pt0) cc_final: 0.8396 (pt0) REVERT: A 237 GLN cc_start: 0.7259 (tp40) cc_final: 0.6846 (mm110) REVERT: A 253 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8173 (t0) REVERT: A 259 MET cc_start: 0.9404 (tpt) cc_final: 0.9120 (tpp) REVERT: A 391 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.7403 (ttm110) REVERT: A 392 ASN cc_start: 0.8082 (m-40) cc_final: 0.7590 (m110) REVERT: A 543 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7687 (mtm-85) REVERT: A 624 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8705 (m) REVERT: A 655 ASP cc_start: 0.6496 (t0) cc_final: 0.6121 (t70) REVERT: B 147 THR cc_start: 0.7040 (m) cc_final: 0.6758 (m) REVERT: B 165 TRP cc_start: 0.8582 (t60) cc_final: 0.8187 (t60) REVERT: B 184 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7191 (mm-30) REVERT: B 253 ILE cc_start: 0.8366 (tt) cc_final: 0.8133 (tt) REVERT: B 256 TYR cc_start: 0.7483 (t80) cc_final: 0.7010 (t80) REVERT: C 62 ARG cc_start: 0.6814 (mmt90) cc_final: 0.6337 (ttp80) REVERT: C 186 ARG cc_start: 0.8510 (ptm-80) cc_final: 0.8193 (ptp-170) REVERT: D 84 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7466 (mtm180) outliers start: 29 outliers final: 18 residues processed: 153 average time/residue: 1.0735 time to fit residues: 181.4230 Evaluate side-chains 148 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101192 restraints weight = 14441.991| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.31 r_work: 0.3089 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11180 Z= 0.253 Angle : 0.626 11.262 15243 Z= 0.303 Chirality : 0.043 0.268 1830 Planarity : 0.004 0.060 1845 Dihedral : 6.935 59.134 2069 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.54 % Allowed : 22.17 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.24), residues: 1322 helix: 1.63 (0.20), residues: 735 sheet: -0.92 (0.46), residues: 121 loop : -1.62 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 36 HIS 0.005 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.025 0.001 TYR B 115 ARG 0.011 0.001 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7740.16 seconds wall clock time: 139 minutes 51.00 seconds (8391.00 seconds total)