Starting phenix.real_space_refine on Sat Aug 23 09:01:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x52_38059/08_2025/8x52_38059.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x52_38059/08_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_38059/08_2025/8x52_38059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x52_38059/08_2025/8x52_38059.map" model { file = "/net/cci-nas-00/data/ceres_data/8x52_38059/08_2025/8x52_38059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x52_38059/08_2025/8x52_38059.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.55, per 1000 atoms: 0.23 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: 0.89 Conformation dependent library (CDL) restraints added in 352.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.29 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: 1.68 Time building geometry restraints manager: 1.11 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: 1.880 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- 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 : 0.017 1.465 11206 Z= 0.918 Angle : 1.455 66.549 15316 Z= 0.771 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 : 7.53 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 626 TYR 0.035 0.003 TYR A 565 PHE 0.040 0.003 PHE B 386 TRP 0.053 0.004 TRP C 227 HIS 0.024 0.003 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00897 (11180) covalent geometry : angle 1.13135 (15243) SS BOND : bond 0.25216 ( 5) SS BOND : angle 21.23594 ( 10) hydrogen bonds : bond 0.19489 ( 579) hydrogen bonds : angle 7.11599 ( 1668) link_BETA1-3 : bond 0.00009 ( 1) link_BETA1-3 : angle 1.61013 ( 3) link_BETA1-4 : bond 0.00225 ( 7) link_BETA1-4 : angle 2.21319 ( 21) link_BETA1-6 : bond 0.00494 ( 1) link_BETA1-6 : angle 1.46481 ( 3) link_NAG-ASN : bond 0.42302 ( 12) link_NAG-ASN : angle 15.17502 ( 36) *********************** 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 : 0.416 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: 0.4283 time to fit residues: 126.4912 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 : 0.391 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3842 r_free = 0.3842 target = 0.150890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120784 restraints weight = 14464.286| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.29 r_work: 0.3351 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11206 Z= 0.170 Angle : 0.706 9.489 15316 Z= 0.341 Chirality : 0.046 0.351 1830 Planarity : 0.005 0.050 1845 Dihedral : 12.268 105.629 2084 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.42 % Allowed : 10.69 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.22), residues: 1322 helix: 0.16 (0.19), residues: 727 sheet: -1.12 (0.49), residues: 109 loop : -2.35 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 520 TYR 0.032 0.002 TYR A 645 PHE 0.040 0.002 PHE A 302 TRP 0.021 0.002 TRP C 209 HIS 0.011 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00385 (11180) covalent geometry : angle 0.67995 (15243) SS BOND : bond 0.01755 ( 5) SS BOND : angle 1.49647 ( 10) hydrogen bonds : bond 0.04724 ( 579) hydrogen bonds : angle 4.56597 ( 1668) link_BETA1-3 : bond 0.00686 ( 1) link_BETA1-3 : angle 2.37408 ( 3) link_BETA1-4 : bond 0.00630 ( 7) link_BETA1-4 : angle 2.17403 ( 21) link_BETA1-6 : bond 0.01816 ( 1) link_BETA1-6 : angle 3.66799 ( 3) link_NAG-ASN : bond 0.01122 ( 12) link_NAG-ASN : angle 3.32625 ( 36) *********************** 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 215 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.6828 (tp) REVERT: A 58 HIS cc_start: 0.8213 (m90) cc_final: 0.7822 (m90) REVERT: A 81 ASP cc_start: 0.6383 (m-30) cc_final: 0.6073 (m-30) REVERT: A 108 MET cc_start: 0.8366 (mmm) cc_final: 0.8144 (mmm) REVERT: A 111 LEU cc_start: 0.7650 (tp) cc_final: 0.7431 (tp) REVERT: A 237 GLN cc_start: 0.6899 (mm-40) cc_final: 0.6480 (tm-30) REVERT: A 391 ARG cc_start: 0.7635 (ttp-110) cc_final: 0.7414 (ttm110) REVERT: A 392 ASN cc_start: 0.8138 (m-40) cc_final: 0.7793 (m-40) REVERT: A 509 ASP cc_start: 0.7465 (m-30) cc_final: 0.6659 (p0) REVERT: A 543 ARG cc_start: 0.7810 (mtm180) cc_final: 0.7531 (mtm110) REVERT: A 617 LEU cc_start: 0.8169 (mp) cc_final: 0.7852 (mm) REVERT: A 624 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8423 (m) REVERT: B 80 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7338 (tptt) REVERT: B 128 ARG cc_start: 0.7712 (mtp180) cc_final: 0.7208 (ttp-170) REVERT: B 154 TYR cc_start: 0.8453 (t80) cc_final: 0.8156 (t80) REVERT: B 163 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7529 (m-70) REVERT: B 165 TRP cc_start: 0.8433 (t60) cc_final: 0.8199 (t60) REVERT: B 169 SER cc_start: 0.8686 (t) cc_final: 0.8164 (p) REVERT: B 184 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6927 (mm-30) REVERT: B 380 LYS cc_start: 0.7339 (mttm) cc_final: 0.6910 (mptt) REVERT: B 463 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8463 (m90) REVERT: C 140 ASP cc_start: 0.8230 (m-30) cc_final: 0.7847 (m-30) REVERT: D 59 ARG cc_start: 0.6673 (ttm170) cc_final: 0.6114 (tmt170) outliers start: 39 outliers final: 17 residues processed: 207 average time/residue: 0.4154 time to fit residues: 94.3956 Evaluate side-chains 154 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 624 THR 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 0 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 57 optimal weight: 0.0000 chunk 94 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.114561 restraints weight = 14525.588| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.28 r_work: 0.3264 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11206 Z= 0.143 Angle : 0.638 9.934 15316 Z= 0.304 Chirality : 0.044 0.392 1830 Planarity : 0.004 0.040 1845 Dihedral : 10.143 111.935 2078 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 4.73 % Allowed : 13.32 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.23), residues: 1322 helix: 0.88 (0.19), residues: 730 sheet: -1.00 (0.47), residues: 116 loop : -1.95 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 434 TYR 0.017 0.001 TYR A 569 PHE 0.035 0.002 PHE A 302 TRP 0.013 0.001 TRP C 209 HIS 0.039 0.002 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00319 (11180) covalent geometry : angle 0.61769 (15243) SS BOND : bond 0.00394 ( 5) SS BOND : angle 0.79785 ( 10) hydrogen bonds : bond 0.04043 ( 579) hydrogen bonds : angle 4.19119 ( 1668) link_BETA1-3 : bond 0.00737 ( 1) link_BETA1-3 : angle 1.45118 ( 3) link_BETA1-4 : bond 0.00459 ( 7) link_BETA1-4 : angle 1.97962 ( 21) link_BETA1-6 : bond 0.01794 ( 1) link_BETA1-6 : angle 2.95440 ( 3) link_NAG-ASN : bond 0.00561 ( 12) link_NAG-ASN : angle 2.90537 ( 36) *********************** 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 189 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.6776 (tp) REVERT: A 58 HIS cc_start: 0.8735 (m90) cc_final: 0.8455 (m90) REVERT: A 391 ARG cc_start: 0.7687 (ttp-110) cc_final: 0.7241 (ttm110) REVERT: A 392 ASN cc_start: 0.8077 (m-40) cc_final: 0.7722 (m-40) REVERT: A 543 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7664 (mtm-85) REVERT: A 598 ASP cc_start: 0.7595 (p0) cc_final: 0.7113 (p0) REVERT: A 617 LEU cc_start: 0.8283 (mp) cc_final: 0.7999 (mm) REVERT: A 693 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7011 (pttt) REVERT: B 128 ARG cc_start: 0.7588 (mtp180) cc_final: 0.7098 (ttp-170) REVERT: B 154 TYR cc_start: 0.8312 (t80) cc_final: 0.7978 (t80) REVERT: B 163 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.7562 (m-70) REVERT: B 177 PHE cc_start: 0.8392 (m-80) cc_final: 0.8149 (m-80) REVERT: B 184 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7529 (mm-30) REVERT: B 380 LYS cc_start: 0.7750 (mttm) cc_final: 0.7313 (mptt) REVERT: C 31 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7796 (mtt180) REVERT: C 62 ARG cc_start: 0.6546 (mmt90) cc_final: 0.5748 (ttp80) REVERT: C 184 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7962 (mtp180) REVERT: C 186 ARG cc_start: 0.8165 (ptp-170) cc_final: 0.7860 (ptp-170) REVERT: C 206 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8078 (mt) REVERT: C 222 VAL cc_start: 0.8313 (t) cc_final: 0.8108 (m) REVERT: D 59 ARG cc_start: 0.7022 (ttm170) cc_final: 0.6333 (tmt170) REVERT: D 84 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6922 (mtm180) outliers start: 54 outliers final: 22 residues processed: 174 average time/residue: 0.4226 time to fit residues: 81.0498 Evaluate side-chains 150 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 46 LYS Chi-restraints excluded: chain A residue 150 ASN 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 693 LYS Chi-restraints excluded: chain A residue 697 LEU 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 79 SER 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 146 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 20 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 444 HIS A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098406 restraints weight = 14659.134| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.29 r_work: 0.3043 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11206 Z= 0.292 Angle : 0.790 11.363 15316 Z= 0.379 Chirality : 0.050 0.359 1830 Planarity : 0.005 0.049 1845 Dihedral : 9.972 104.587 2074 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.87 % Allowed : 14.64 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.23), residues: 1322 helix: 0.76 (0.19), residues: 741 sheet: -1.10 (0.45), residues: 122 loop : -2.03 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 583 TYR 0.028 0.003 TYR A 499 PHE 0.037 0.003 PHE A 302 TRP 0.027 0.002 TRP C 209 HIS 0.012 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00701 (11180) covalent geometry : angle 0.76596 (15243) SS BOND : bond 0.00768 ( 5) SS BOND : angle 1.52202 ( 10) hydrogen bonds : bond 0.04754 ( 579) hydrogen bonds : angle 4.39338 ( 1668) link_BETA1-3 : bond 0.00620 ( 1) link_BETA1-3 : angle 1.81032 ( 3) link_BETA1-4 : bond 0.00521 ( 7) link_BETA1-4 : angle 2.46125 ( 21) link_BETA1-6 : bond 0.01341 ( 1) link_BETA1-6 : angle 3.25954 ( 3) link_NAG-ASN : bond 0.01250 ( 12) link_NAG-ASN : angle 3.42194 ( 36) *********************** 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 208 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 141 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 118 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 231 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8395 (mmm) REVERT: A 249 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7657 (OUTLIER) REVERT: A 391 ARG cc_start: 0.7777 (ttp-110) cc_final: 0.7503 (ttp-110) REVERT: A 392 ASN cc_start: 0.8042 (m-40) cc_final: 0.7734 (m-40) REVERT: A 466 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8382 (p) REVERT: A 540 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7952 (tp40) REVERT: A 543 ARG cc_start: 0.7870 (mtm180) cc_final: 0.7504 (mtm110) REVERT: A 585 GLN cc_start: 0.7833 (mt0) cc_final: 0.7458 (mt0) REVERT: A 617 LEU cc_start: 0.8392 (mp) cc_final: 0.8184 (mm) REVERT: A 624 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8870 (m) REVERT: A 655 ASP cc_start: 0.6867 (t0) cc_final: 0.6500 (t70) REVERT: A 666 LYS cc_start: 0.7382 (tptt) cc_final: 0.6834 (ttpt) REVERT: A 677 PHE cc_start: 0.8247 (m-80) cc_final: 0.8011 (m-10) REVERT: B 80 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7443 (tppt) REVERT: B 177 PHE cc_start: 0.8419 (m-80) cc_final: 0.8191 (m-80) REVERT: B 184 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7737 (mm-30) REVERT: B 253 ILE cc_start: 0.8390 (tt) cc_final: 0.8179 (tt) REVERT: B 424 LEU cc_start: 0.7803 (mp) cc_final: 0.7587 (mm) REVERT: B 429 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8266 (mtmm) REVERT: C 121 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8743 (p) REVERT: C 186 ARG cc_start: 0.8233 (ptp-170) cc_final: 0.8013 (ptp-170) REVERT: C 206 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8390 (mt) REVERT: C 236 LEU cc_start: 0.8105 (mm) cc_final: 0.7781 (tp) REVERT: D 59 ARG cc_start: 0.7628 (ttm170) cc_final: 0.6790 (tmt170) REVERT: D 65 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6835 (tm) REVERT: D 84 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7394 (mtm180) outliers start: 67 outliers final: 22 residues processed: 192 average time/residue: 0.4140 time to fit residues: 86.9900 Evaluate side-chains 153 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 231 MET 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 466 SER Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 149 LEU 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 121 SER Chi-restraints excluded: chain C residue 123 LEU 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 65 LEU Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 70 VAL 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 107 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 51 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS 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 = 0.3653 r_free = 0.3653 target = 0.134124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102302 restraints weight = 14565.715| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.26 r_work: 0.3105 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11206 Z= 0.132 Angle : 0.636 11.546 15316 Z= 0.299 Chirality : 0.043 0.284 1830 Planarity : 0.004 0.037 1845 Dihedral : 9.177 96.003 2072 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 3.86 % Allowed : 17.70 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.23), residues: 1322 helix: 1.31 (0.20), residues: 731 sheet: -1.02 (0.46), residues: 123 loop : -1.77 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.020 0.001 TYR A 499 PHE 0.031 0.001 PHE A 302 TRP 0.014 0.001 TRP D 74 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00300 (11180) covalent geometry : angle 0.61607 (15243) SS BOND : bond 0.00953 ( 5) SS BOND : angle 0.71820 ( 10) hydrogen bonds : bond 0.03718 ( 579) hydrogen bonds : angle 4.10658 ( 1668) link_BETA1-3 : bond 0.00641 ( 1) link_BETA1-3 : angle 1.68040 ( 3) link_BETA1-4 : bond 0.00351 ( 7) link_BETA1-4 : angle 1.88281 ( 21) link_BETA1-6 : bond 0.01581 ( 1) link_BETA1-6 : angle 3.32801 ( 3) link_NAG-ASN : bond 0.00408 ( 12) link_NAG-ASN : angle 2.87224 ( 36) *********************** 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 177 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: E 31 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.6694 (tp) REVERT: A 37 GLU cc_start: 0.8429 (pt0) cc_final: 0.8187 (pt0) REVERT: A 118 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8424 (mp) REVERT: A 249 ASP cc_start: 0.8128 (t0) cc_final: 0.7606 (p0) REVERT: A 253 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8445 (t0) REVERT: A 259 MET cc_start: 0.9162 (mmm) cc_final: 0.8890 (tpt) REVERT: A 391 ARG cc_start: 0.7733 (ttp-110) cc_final: 0.7465 (ttm110) REVERT: A 392 ASN cc_start: 0.8032 (m-40) cc_final: 0.7747 (m-40) REVERT: A 482 ASP cc_start: 0.7833 (m-30) cc_final: 0.7440 (m-30) REVERT: A 540 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7910 (tp40) REVERT: A 543 ARG cc_start: 0.7751 (mtm180) cc_final: 0.7376 (mtm110) REVERT: A 582 THR cc_start: 0.7438 (OUTLIER) cc_final: 0.7221 (m) REVERT: A 624 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8677 (m) REVERT: A 655 ASP cc_start: 0.6478 (t0) cc_final: 0.5936 (t70) REVERT: A 677 PHE cc_start: 0.8296 (m-80) cc_final: 0.7986 (m-10) REVERT: B 253 ILE cc_start: 0.8334 (tt) cc_final: 0.8091 (tt) REVERT: B 390 SER cc_start: 0.8918 (m) cc_final: 0.8713 (p) REVERT: C 62 ARG cc_start: 0.6343 (mmt-90) cc_final: 0.5767 (ttp80) REVERT: C 186 ARG cc_start: 0.8136 (ptp-170) cc_final: 0.7825 (ptp-170) REVERT: C 206 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7982 (mt) REVERT: D 59 ARG cc_start: 0.7576 (ttm170) cc_final: 0.6635 (tmt170) REVERT: D 84 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7257 (mtm180) outliers start: 44 outliers final: 14 residues processed: 167 average time/residue: 0.4092 time to fit residues: 75.0144 Evaluate side-chains 146 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ILE 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 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 582 THR 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 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 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 72 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 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 = 0.3627 r_free = 0.3627 target = 0.131987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099573 restraints weight = 14590.634| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.30 r_work: 0.3068 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11206 Z= 0.189 Angle : 0.667 11.088 15316 Z= 0.317 Chirality : 0.044 0.280 1830 Planarity : 0.004 0.042 1845 Dihedral : 8.884 80.222 2072 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 4.03 % Allowed : 18.14 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.23), residues: 1322 helix: 1.38 (0.20), residues: 731 sheet: -1.06 (0.45), residues: 121 loop : -1.76 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 583 TYR 0.020 0.002 TYR A 499 PHE 0.032 0.002 PHE A 302 TRP 0.013 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00454 (11180) covalent geometry : angle 0.64765 (15243) SS BOND : bond 0.00505 ( 5) SS BOND : angle 2.13753 ( 10) hydrogen bonds : bond 0.03844 ( 579) hydrogen bonds : angle 4.09699 ( 1668) link_BETA1-3 : bond 0.00537 ( 1) link_BETA1-3 : angle 1.63180 ( 3) link_BETA1-4 : bond 0.00329 ( 7) link_BETA1-4 : angle 1.90152 ( 21) link_BETA1-6 : bond 0.01346 ( 1) link_BETA1-6 : angle 3.35863 ( 3) link_NAG-ASN : bond 0.00457 ( 12) link_NAG-ASN : angle 2.68841 ( 36) *********************** 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 180 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8247 (tp) REVERT: A 37 GLU cc_start: 0.8528 (pt0) cc_final: 0.8276 (pt0) REVERT: A 118 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8468 (mp) REVERT: A 249 ASP cc_start: 0.8086 (t0) cc_final: 0.7656 (p0) REVERT: A 253 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8587 (t0) REVERT: A 391 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7345 (ttm110) REVERT: A 392 ASN cc_start: 0.8048 (m-40) cc_final: 0.7681 (m-40) REVERT: A 482 ASP cc_start: 0.7840 (m-30) cc_final: 0.7528 (m-30) REVERT: A 543 ARG cc_start: 0.7789 (mtm180) cc_final: 0.7499 (mtm-85) REVERT: A 624 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8785 (m) REVERT: A 655 ASP cc_start: 0.6697 (t0) cc_final: 0.6151 (t70) REVERT: A 677 PHE cc_start: 0.8318 (m-80) cc_final: 0.7988 (m-10) REVERT: B 147 THR cc_start: 0.7065 (m) cc_final: 0.6716 (m) REVERT: B 165 TRP cc_start: 0.8557 (t60) cc_final: 0.8096 (t60) REVERT: B 253 ILE cc_start: 0.8352 (tt) cc_final: 0.8121 (tt) REVERT: B 457 MET cc_start: 0.9228 (tpp) cc_final: 0.8985 (mmt) REVERT: C 31 ARG cc_start: 0.8267 (mtt180) cc_final: 0.8041 (mtt180) REVERT: C 62 ARG cc_start: 0.6429 (mmt-90) cc_final: 0.5930 (ttp80) REVERT: C 186 ARG cc_start: 0.8157 (ptp-170) cc_final: 0.7903 (ptm-80) REVERT: C 206 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8036 (mt) REVERT: D 59 ARG cc_start: 0.7627 (ttm170) cc_final: 0.6773 (mmt180) REVERT: D 84 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7361 (mtm180) outliers start: 46 outliers final: 20 residues processed: 167 average time/residue: 0.5202 time to fit residues: 94.5246 Evaluate side-chains 153 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 41 ILE 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 253 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 622 ARG 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 B residue 289 SER Chi-restraints excluded: chain B residue 420 LEU 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 C residue 223 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 36 optimal weight: 0.0970 chunk 88 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 104 optimal weight: 0.0070 chunk 58 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 124 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 585 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 = 0.3672 r_free = 0.3672 target = 0.135766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.103866 restraints weight = 14499.497| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.30 r_work: 0.3127 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11206 Z= 0.107 Angle : 0.600 11.242 15316 Z= 0.282 Chirality : 0.042 0.273 1830 Planarity : 0.004 0.042 1845 Dihedral : 8.222 62.762 2072 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.42 % Favored : 97.50 % Rotamer: Outliers : 2.63 % Allowed : 19.28 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.24), residues: 1322 helix: 1.63 (0.20), residues: 730 sheet: -0.95 (0.46), residues: 123 loop : -1.61 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 237 TYR 0.017 0.001 TYR A 499 PHE 0.029 0.001 PHE A 302 TRP 0.011 0.001 TRP D 74 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00231 (11180) covalent geometry : angle 0.58409 (15243) SS BOND : bond 0.00320 ( 5) SS BOND : angle 1.57290 ( 10) hydrogen bonds : bond 0.03252 ( 579) hydrogen bonds : angle 3.95432 ( 1668) link_BETA1-3 : bond 0.00649 ( 1) link_BETA1-3 : angle 1.42911 ( 3) link_BETA1-4 : bond 0.00416 ( 7) link_BETA1-4 : angle 1.50563 ( 21) link_BETA1-6 : bond 0.00997 ( 1) link_BETA1-6 : angle 3.41903 ( 3) link_NAG-ASN : bond 0.00423 ( 12) link_NAG-ASN : angle 2.32648 ( 36) *********************** 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 167 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8198 (tp) REVERT: A 37 GLU cc_start: 0.8516 (pt0) cc_final: 0.8256 (pt0) REVERT: A 118 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 237 GLN cc_start: 0.7297 (tp40) cc_final: 0.6793 (mm110) REVERT: A 249 ASP cc_start: 0.8086 (t0) cc_final: 0.7758 (p0) REVERT: A 253 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8380 (t70) REVERT: A 391 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7300 (ttm110) REVERT: A 392 ASN cc_start: 0.7981 (m-40) cc_final: 0.7610 (m-40) REVERT: A 482 ASP cc_start: 0.7727 (m-30) cc_final: 0.7409 (m-30) REVERT: A 543 ARG cc_start: 0.7775 (mtm180) cc_final: 0.7493 (mtm-85) REVERT: A 582 THR cc_start: 0.8009 (m) cc_final: 0.7735 (p) REVERT: A 624 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8579 (m) REVERT: A 655 ASP cc_start: 0.6298 (t0) cc_final: 0.5754 (t70) REVERT: A 677 PHE cc_start: 0.8325 (m-80) cc_final: 0.7938 (m-10) REVERT: B 147 THR cc_start: 0.6952 (m) cc_final: 0.6617 (m) REVERT: B 165 TRP cc_start: 0.8522 (t60) cc_final: 0.7956 (t60) REVERT: B 253 ILE cc_start: 0.8344 (tt) cc_final: 0.8103 (tt) REVERT: B 457 MET cc_start: 0.9182 (tpp) cc_final: 0.8944 (mmt) REVERT: C 62 ARG cc_start: 0.6391 (mmt-90) cc_final: 0.5925 (ttp80) REVERT: D 59 ARG cc_start: 0.7637 (ttm170) cc_final: 0.6774 (mmt180) REVERT: D 84 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7362 (mtm180) outliers start: 30 outliers final: 13 residues processed: 161 average time/residue: 0.4293 time to fit residues: 75.9740 Evaluate side-chains 143 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE 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 253 ASP Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain B residue 113 LEU 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 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 4 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 103 optimal weight: 0.0670 chunk 56 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.134779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102986 restraints weight = 14519.178| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.29 r_work: 0.3098 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11206 Z= 0.128 Angle : 0.599 11.217 15316 Z= 0.287 Chirality : 0.042 0.277 1830 Planarity : 0.004 0.042 1845 Dihedral : 7.817 64.414 2071 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 2.63 % Allowed : 20.51 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.24), residues: 1322 helix: 1.69 (0.20), residues: 736 sheet: -0.95 (0.45), residues: 121 loop : -1.66 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 237 TYR 0.020 0.001 TYR B 115 PHE 0.036 0.002 PHE B 105 TRP 0.011 0.001 TRP B 244 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00299 (11180) covalent geometry : angle 0.58447 (15243) SS BOND : bond 0.00320 ( 5) SS BOND : angle 1.39651 ( 10) hydrogen bonds : bond 0.03307 ( 579) hydrogen bonds : angle 3.89900 ( 1668) link_BETA1-3 : bond 0.00657 ( 1) link_BETA1-3 : angle 1.40118 ( 3) link_BETA1-4 : bond 0.00301 ( 7) link_BETA1-4 : angle 1.56812 ( 21) link_BETA1-6 : bond 0.00925 ( 1) link_BETA1-6 : angle 3.08384 ( 3) link_NAG-ASN : bond 0.00343 ( 12) link_NAG-ASN : angle 2.29643 ( 36) *********************** 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 166 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 118 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8411 (mp) REVERT: A 156 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: A 237 GLN cc_start: 0.7204 (tp40) cc_final: 0.6720 (mm110) REVERT: A 249 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7736 (OUTLIER) REVERT: A 253 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8318 (t0) REVERT: A 391 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7345 (ttm110) REVERT: A 392 ASN cc_start: 0.7949 (m-40) cc_final: 0.7573 (m-40) REVERT: A 543 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7579 (mtm-85) REVERT: A 624 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8701 (m) REVERT: A 655 ASP cc_start: 0.6655 (t0) cc_final: 0.6123 (t70) REVERT: A 677 PHE cc_start: 0.8346 (m-80) cc_final: 0.8026 (m-10) REVERT: B 130 LEU cc_start: 0.7762 (mm) cc_final: 0.7353 (mm) REVERT: B 147 THR cc_start: 0.6978 (m) cc_final: 0.6732 (m) REVERT: B 165 TRP cc_start: 0.8581 (t60) cc_final: 0.8203 (t60) REVERT: B 253 ILE cc_start: 0.8334 (tt) cc_final: 0.8111 (tt) REVERT: B 256 TYR cc_start: 0.7469 (t80) cc_final: 0.7044 (t80) REVERT: B 457 MET cc_start: 0.9171 (tpp) cc_final: 0.8967 (mmt) REVERT: C 55 ILE cc_start: 0.7540 (mt) cc_final: 0.7243 (mt) REVERT: C 62 ARG cc_start: 0.6422 (mmt-90) cc_final: 0.5993 (ttp80) REVERT: D 49 GLU cc_start: 0.8114 (pm20) cc_final: 0.7881 (mp0) REVERT: D 59 ARG cc_start: 0.7558 (ttm170) cc_final: 0.6769 (mmt180) REVERT: D 84 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7321 (mtm180) outliers start: 30 outliers final: 16 residues processed: 160 average time/residue: 0.4719 time to fit residues: 82.7424 Evaluate side-chains 148 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 156 PHE 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 624 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 223 SER 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 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 38 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 104 optimal weight: 0.0170 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.134617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103135 restraints weight = 14378.430| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.24 r_work: 0.3116 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11206 Z= 0.126 Angle : 0.596 11.263 15316 Z= 0.284 Chirality : 0.042 0.273 1830 Planarity : 0.004 0.064 1845 Dihedral : 7.521 57.310 2071 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 2.28 % Allowed : 21.30 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.24), residues: 1322 helix: 1.73 (0.20), residues: 736 sheet: -1.03 (0.44), residues: 123 loop : -1.63 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 237 TYR 0.021 0.001 TYR B 115 PHE 0.029 0.001 PHE A 302 TRP 0.010 0.001 TRP B 244 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00296 (11180) covalent geometry : angle 0.58191 (15243) SS BOND : bond 0.00299 ( 5) SS BOND : angle 1.36035 ( 10) hydrogen bonds : bond 0.03247 ( 579) hydrogen bonds : angle 3.87932 ( 1668) link_BETA1-3 : bond 0.00664 ( 1) link_BETA1-3 : angle 1.44525 ( 3) link_BETA1-4 : bond 0.00289 ( 7) link_BETA1-4 : angle 1.51668 ( 21) link_BETA1-6 : bond 0.00887 ( 1) link_BETA1-6 : angle 2.86699 ( 3) link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 2.22685 ( 36) *********************** 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 152 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.9007 (mmm) cc_final: 0.8406 (mmm) REVERT: A 156 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8174 (m-80) REVERT: A 237 GLN cc_start: 0.7203 (tp40) cc_final: 0.6724 (mm110) REVERT: A 249 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7747 (p0) REVERT: A 253 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8409 (t0) REVERT: A 391 ARG cc_start: 0.7648 (ttp-110) cc_final: 0.7371 (ttm110) REVERT: A 392 ASN cc_start: 0.7959 (m-40) cc_final: 0.7599 (m-40) REVERT: A 543 ARG cc_start: 0.7813 (mtm180) cc_final: 0.7546 (mtm-85) REVERT: A 582 THR cc_start: 0.8080 (m) cc_final: 0.7744 (p) REVERT: A 624 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8690 (m) REVERT: A 655 ASP cc_start: 0.6467 (t0) cc_final: 0.5940 (t70) REVERT: A 677 PHE cc_start: 0.8354 (m-80) cc_final: 0.8008 (m-10) REVERT: B 130 LEU cc_start: 0.7741 (mm) cc_final: 0.7402 (mm) REVERT: B 147 THR cc_start: 0.6975 (m) cc_final: 0.6618 (m) REVERT: B 165 TRP cc_start: 0.8580 (t60) cc_final: 0.8105 (t60) REVERT: B 253 ILE cc_start: 0.8349 (tt) cc_final: 0.8113 (tt) REVERT: B 457 MET cc_start: 0.9166 (tpp) cc_final: 0.8963 (mmt) REVERT: C 55 ILE cc_start: 0.7566 (mt) cc_final: 0.7285 (mt) REVERT: C 62 ARG cc_start: 0.6464 (mmt-90) cc_final: 0.6064 (ttp80) REVERT: D 59 ARG cc_start: 0.7567 (ttm170) cc_final: 0.6781 (mmt180) REVERT: D 65 LEU cc_start: 0.7312 (tm) cc_final: 0.7082 (tp) REVERT: D 84 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7341 (mtm180) outliers start: 26 outliers final: 13 residues processed: 145 average time/residue: 0.4961 time to fit residues: 78.8668 Evaluate side-chains 140 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 156 PHE 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 624 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 58 TRP 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 31 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 85 optimal weight: 0.0980 chunk 110 optimal weight: 0.0980 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104094 restraints weight = 14444.218| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.30 r_work: 0.3125 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11206 Z= 0.114 Angle : 0.593 11.009 15316 Z= 0.282 Chirality : 0.042 0.275 1830 Planarity : 0.004 0.056 1845 Dihedral : 7.087 58.433 2069 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 2.02 % Allowed : 22.00 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.24), residues: 1322 helix: 1.86 (0.20), residues: 730 sheet: -1.01 (0.44), residues: 123 loop : -1.47 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.016 0.001 TYR A 569 PHE 0.030 0.001 PHE A 302 TRP 0.009 0.001 TRP D 58 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00262 (11180) covalent geometry : angle 0.58087 (15243) SS BOND : bond 0.00254 ( 5) SS BOND : angle 1.29330 ( 10) hydrogen bonds : bond 0.03088 ( 579) hydrogen bonds : angle 3.83254 ( 1668) link_BETA1-3 : bond 0.00685 ( 1) link_BETA1-3 : angle 1.38570 ( 3) link_BETA1-4 : bond 0.00284 ( 7) link_BETA1-4 : angle 1.43919 ( 21) link_BETA1-6 : bond 0.00905 ( 1) link_BETA1-6 : angle 2.39003 ( 3) link_NAG-ASN : bond 0.00322 ( 12) link_NAG-ASN : angle 2.10023 ( 36) ********************** 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 153 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 108 MET cc_start: 0.9007 (mmm) cc_final: 0.8515 (mmm) REVERT: A 156 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: A 237 GLN cc_start: 0.7143 (tp40) cc_final: 0.6776 (mm110) REVERT: A 249 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7763 (p0) REVERT: A 253 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8315 (t70) REVERT: A 391 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.7338 (ttm110) REVERT: A 392 ASN cc_start: 0.7971 (m-40) cc_final: 0.7498 (m110) REVERT: A 543 ARG cc_start: 0.7782 (mtm180) cc_final: 0.7529 (mtm-85) REVERT: A 582 THR cc_start: 0.8083 (m) cc_final: 0.7749 (p) REVERT: A 624 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8505 (m) REVERT: A 655 ASP cc_start: 0.6508 (t0) cc_final: 0.5987 (t70) REVERT: B 130 LEU cc_start: 0.7519 (mm) cc_final: 0.7179 (mm) REVERT: B 147 THR cc_start: 0.6908 (m) cc_final: 0.6556 (m) REVERT: B 165 TRP cc_start: 0.8636 (t60) cc_final: 0.8253 (t60) REVERT: B 253 ILE cc_start: 0.8156 (tt) cc_final: 0.7921 (tt) REVERT: C 62 ARG cc_start: 0.6485 (mmt-90) cc_final: 0.6085 (ttp80) REVERT: D 59 ARG cc_start: 0.7599 (ttm170) cc_final: 0.6759 (mmt180) REVERT: D 65 LEU cc_start: 0.7311 (tm) cc_final: 0.6995 (tt) REVERT: D 84 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7350 (mtm180) outliers start: 23 outliers final: 12 residues processed: 148 average time/residue: 0.4982 time to fit residues: 81.1212 Evaluate side-chains 142 residues out of total 1142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 156 PHE 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 624 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 223 SER 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 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101681 restraints weight = 14454.074| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.31 r_work: 0.3096 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11206 Z= 0.144 Angle : 0.608 11.050 15316 Z= 0.292 Chirality : 0.043 0.272 1830 Planarity : 0.004 0.055 1845 Dihedral : 6.938 57.666 2069 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Rotamer: Outliers : 2.10 % Allowed : 22.35 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1322 helix: 1.75 (0.20), residues: 737 sheet: -0.95 (0.44), residues: 121 loop : -1.57 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 237 TYR 0.016 0.001 TYR A 569 PHE 0.030 0.002 PHE A 302 TRP 0.011 0.001 TRP B 244 HIS 0.005 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00342 (11180) covalent geometry : angle 0.59531 (15243) SS BOND : bond 0.00354 ( 5) SS BOND : angle 1.30925 ( 10) hydrogen bonds : bond 0.03340 ( 579) hydrogen bonds : angle 3.89048 ( 1668) link_BETA1-3 : bond 0.00567 ( 1) link_BETA1-3 : angle 1.57203 ( 3) link_BETA1-4 : bond 0.00257 ( 7) link_BETA1-4 : angle 1.56948 ( 21) link_BETA1-6 : bond 0.00827 ( 1) link_BETA1-6 : angle 1.82638 ( 3) link_NAG-ASN : bond 0.00363 ( 12) link_NAG-ASN : angle 2.17264 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3736.75 seconds wall clock time: 64 minutes 22.86 seconds (3862.86 seconds total)