Starting phenix.real_space_refine on Sat Aug 23 08:54:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x54_38061/08_2025/8x54_38061.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x54_38061/08_2025/8x54_38061.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/8x54_38061/08_2025/8x54_38061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x54_38061/08_2025/8x54_38061.map" model { file = "/net/cci-nas-00/data/ceres_data/8x54_38061/08_2025/8x54_38061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x54_38061/08_2025/8x54_38061.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= 0.019 sd= 0.147 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 3 5.49 5 S 44 5.16 5 C 7223 2.51 5 N 1734 2.21 5 O 2005 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: 11009 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 178 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 2.32, per 1000 atoms: 0.21 Number of scatterers: 11009 At special positions: 0 Unit cell: (108.692, 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 44 16.00 P 3 15.00 O 2005 8.00 N 1734 7.00 C 7223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS A 242 " distance=2.03 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: 0.67 Conformation dependent library (CDL) restraints added in 364.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 7 sheets defined 58.8% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'E' and resid 31 through 43 removed outlier: 3.657A pdb=" N GLY E 37 " --> pdb=" O GLY E 33 " (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: 3.598A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 3.889A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.662A 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: 3.698A 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: 3.528A 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: 3.750A 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: 3.752A pdb=" N ILE B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 84 " --> pdb=" O LYS B 80 " (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: 3.596A pdb=" N LEU B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.847A 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: 3.920A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.500A 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 383 through 399 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: 3.978A 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: 3.752A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 3.794A pdb=" N THR B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 442 " --> pdb=" O SER B 438 " (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: 3.904A 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: 3.637A 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: 3.738A 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: 3.535A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.079A 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: 3.635A 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: 3.592A 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: 4.130A 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 'E' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'E' and resid 53 through 54 removed outlier: 4.355A pdb=" N GLY B 378 " --> pdb=" O LYS E 54 " (cutoff:3.500A) Processing sheet with id=AA3, 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: 6.530A 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: 6.776A 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: 8.299A 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=AA4, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.549A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 9.043A 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: 7.673A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.568A 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: 6.354A 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: 7.693A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, 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=AA7, 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) 580 hydrogen bonds defined for protein. 1680 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: 1.32 Time building geometry restraints manager: 0.89 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: 86 1.23 - 1.37: 3611 1.37 - 1.52: 5087 1.52 - 1.67: 2433 1.67 - 1.81: 67 Bond restraints: 11284 Sorted by residual: bond pdb=" C LEU B 241 " pdb=" N PRO B 242 " ideal model delta sigma weight residual 1.331 1.512 -0.181 1.21e-02 6.83e+03 2.24e+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 ALA B 434 " pdb=" O ALA B 434 " ideal model delta sigma weight residual 1.236 1.388 -0.152 1.19e-02 7.06e+03 1.64e+02 bond pdb=" C ILE B 437 " pdb=" O ILE B 437 " ideal model delta sigma weight residual 1.240 1.095 0.144 1.18e-02 7.18e+03 1.49e+02 bond pdb=" C SER B 438 " pdb=" O SER B 438 " ideal model delta sigma weight residual 1.236 1.081 0.155 1.29e-02 6.01e+03 1.44e+02 ... (remaining 11279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 15298 5.73 - 11.47: 68 11.47 - 17.20: 12 17.20 - 22.93: 1 22.93 - 28.67: 1 Bond angle restraints: 15380 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 115.43 144.10 -28.67 1.41e+00 5.03e-01 4.13e+02 angle pdb=" C THR B 116 " pdb=" N PRO B 117 " pdb=" CA PRO B 117 " ideal model delta sigma weight residual 119.84 137.84 -18.00 1.25e+00 6.40e-01 2.07e+02 angle pdb=" C LEU B 435 " pdb=" N PRO B 436 " pdb=" CA PRO B 436 " ideal model delta sigma weight residual 119.24 131.58 -12.34 1.04e+00 9.25e-01 1.41e+02 angle pdb=" CA THR B 116 " pdb=" C THR B 116 " pdb=" N PRO B 117 " ideal model delta sigma weight residual 117.57 127.64 -10.07 8.70e-01 1.32e+00 1.34e+02 angle pdb=" C ALA B 79 " pdb=" N LYS B 80 " pdb=" CA LYS B 80 " ideal model delta sigma weight residual 120.44 133.39 -12.95 1.30e+00 5.92e-01 9.93e+01 ... (remaining 15375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 6726 23.50 - 47.00: 228 47.00 - 70.49: 53 70.49 - 93.99: 21 93.99 - 117.49: 18 Dihedral angle restraints: 7046 sinusoidal: 3149 harmonic: 3897 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 -104.14 -18.46 0 2.50e+00 1.60e-01 5.45e+01 dihedral pdb=" C GLN B 112 " pdb=" N GLN B 112 " pdb=" CA GLN B 112 " pdb=" CB GLN B 112 " ideal model delta harmonic sigma weight residual -122.60 -106.11 -16.49 0 2.50e+00 1.60e-01 4.35e+01 ... (remaining 7043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1778 0.134 - 0.268: 49 0.268 - 0.402: 14 0.402 - 0.536: 2 0.536 - 0.670: 1 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CB VAL E 46 " pdb=" CA VAL E 46 " pdb=" CG1 VAL E 46 " pdb=" CG2 VAL E 46 " both_signs ideal model delta sigma weight residual False -2.63 -1.96 -0.67 2.00e-01 2.50e+01 1.12e+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 6.57e+00 chirality pdb=" CA VAL E 46 " pdb=" N VAL E 46 " pdb=" C VAL E 46 " pdb=" CB VAL E 46 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 1841 not shown) Planarity restraints: 1862 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 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " -0.188 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " -0.014 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 439 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ILE B 439 " -0.070 2.00e-02 2.50e+03 pdb=" O ILE B 439 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 440 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 112 " -0.019 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C GLN B 112 " 0.069 2.00e-02 2.50e+03 pdb=" O GLN B 112 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU B 113 " -0.023 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 2 2.26 - 2.92: 4408 2.92 - 3.58: 15386 3.58 - 4.24: 25471 4.24 - 4.90: 42993 Nonbonded interactions: 88260 Sorted by model distance: nonbonded pdb=" OD1 ASN A 573 " pdb=" C1 NAG I 1 " model vdw 1.597 2.776 nonbonded pdb=" O VAL E 39 " pdb=" OG1 THR E 43 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.264 3.040 nonbonded pdb=" O PRO A 130 " pdb=" OH TYR A 452 " model vdw 2.297 3.040 nonbonded pdb=" OG SER A 202 " pdb=" O SER A 206 " model vdw 2.311 3.040 ... (remaining 88255 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: 0.370 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.510 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 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 11310 Z= 0.904 Angle : 1.364 61.435 15453 Z= 0.724 Chirality : 0.068 0.670 1844 Planarity : 0.007 0.071 1850 Dihedral : 14.622 117.489 4519 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.05 % Allowed : 2.79 % Favored : 96.16 % Cbeta Deviations : 0.48 % 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: -3.47 (0.18), residues: 1325 helix: -1.89 (0.15), residues: 728 sheet: -1.54 (0.47), residues: 114 loop : -2.97 (0.23), residues: 483 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 0.00971 (11284) covalent geometry : angle 1.14922 (15380) SS BOND : bond 0.00641 ( 5) SS BOND : angle 2.15695 ( 10) hydrogen bonds : bond 0.19362 ( 580) hydrogen bonds : angle 7.02869 ( 1680) link_BETA1-3 : bond 0.00002 ( 1) link_BETA1-3 : angle 1.60727 ( 3) link_BETA1-4 : bond 0.00217 ( 7) link_BETA1-4 : angle 2.21426 ( 21) link_BETA1-6 : bond 0.00496 ( 1) link_BETA1-6 : angle 1.46826 ( 3) link_NAG-ASN : bond 0.42309 ( 12) link_NAG-ASN : angle 15.17694 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 241 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: E 41 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6521 (mp) REVERT: A 46 LYS cc_start: 0.6443 (mmmm) cc_final: 0.5864 (mmtm) REVERT: A 58 HIS cc_start: 0.6605 (m90) cc_final: 0.6042 (m90) REVERT: A 77 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7376 (mm-30) REVERT: A 78 LYS cc_start: 0.6246 (ptpt) cc_final: 0.5801 (pttm) REVERT: A 81 ASP cc_start: 0.6419 (m-30) cc_final: 0.6081 (m-30) REVERT: A 94 TYR cc_start: 0.7197 (m-80) cc_final: 0.6732 (m-80) REVERT: A 155 GLU cc_start: 0.7276 (mp0) cc_final: 0.7004 (mp0) REVERT: A 221 MET cc_start: 0.7019 (mmp) cc_final: 0.6772 (mmp) REVERT: A 284 SER cc_start: 0.8339 (p) cc_final: 0.8062 (m) REVERT: A 344 VAL cc_start: 0.5933 (t) cc_final: 0.5636 (t) REVERT: A 351 LYS cc_start: 0.7031 (mmtp) cc_final: 0.6802 (mtpt) REVERT: A 528 LYS cc_start: 0.6068 (tttt) cc_final: 0.5812 (tttm) REVERT: A 531 ASN cc_start: 0.6002 (m-40) cc_final: 0.5799 (m-40) REVERT: A 606 GLN cc_start: 0.5167 (mt0) cc_final: 0.4879 (mt0) REVERT: A 693 LYS cc_start: 0.6922 (mmtp) cc_final: 0.6660 (mmmm) REVERT: B 430 LYS cc_start: 0.6481 (mtpt) cc_final: 0.5541 (pttt) REVERT: B 436 PRO cc_start: 0.7053 (OUTLIER) cc_final: 0.6835 (Cg_exo) REVERT: C 28 ASP cc_start: 0.6885 (m-30) cc_final: 0.6666 (t0) REVERT: C 29 PRO cc_start: 0.7362 (Cg_endo) cc_final: 0.7125 (Cg_exo) REVERT: C 113 SER cc_start: 0.6085 (m) cc_final: 0.5774 (p) REVERT: C 183 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6827 (tp30) outliers start: 12 outliers final: 2 residues processed: 247 average time/residue: 0.5017 time to fit residues: 135.4874 Evaluate side-chains 139 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 436 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 158 HIS A 163 GLN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 420 GLN A 454 GLN A 531 ASN A 535 GLN A 606 GLN B 385 ASN B 463 HIS C 68 GLN D 8 ASN D 33 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128649 restraints weight = 13238.262| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.35 r_work: 0.3382 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11310 Z= 0.135 Angle : 0.671 12.357 15453 Z= 0.325 Chirality : 0.044 0.284 1844 Planarity : 0.005 0.042 1850 Dihedral : 13.099 102.467 2180 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.79 % Allowed : 10.73 % Favored : 86.47 % 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: -1.22 (0.22), residues: 1325 helix: 0.30 (0.19), residues: 724 sheet: -1.07 (0.49), residues: 108 loop : -2.44 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.014 0.001 TYR A 569 PHE 0.035 0.002 PHE A 302 TRP 0.018 0.001 TRP C 227 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00286 (11284) covalent geometry : angle 0.64587 (15380) SS BOND : bond 0.00525 ( 5) SS BOND : angle 1.44625 ( 10) hydrogen bonds : bond 0.05101 ( 580) hydrogen bonds : angle 4.66385 ( 1680) link_BETA1-3 : bond 0.00867 ( 1) link_BETA1-3 : angle 2.28455 ( 3) link_BETA1-4 : bond 0.00565 ( 7) link_BETA1-4 : angle 1.83983 ( 21) link_BETA1-6 : bond 0.01800 ( 1) link_BETA1-6 : angle 2.88582 ( 3) link_NAG-ASN : bond 0.00632 ( 12) link_NAG-ASN : angle 3.37779 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.637 Fit side-chains REVERT: A 46 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7878 (mmtm) REVERT: A 78 LYS cc_start: 0.7498 (ptpt) cc_final: 0.7144 (pttm) REVERT: A 235 SER cc_start: 0.7511 (t) cc_final: 0.7202 (p) REVERT: A 364 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.6670 (tt0) REVERT: A 395 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 528 LYS cc_start: 0.8211 (tttt) cc_final: 0.7887 (tttm) REVERT: B 84 MET cc_start: 0.8395 (mtp) cc_final: 0.8187 (mtt) REVERT: B 180 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8153 (mm) REVERT: B 283 PHE cc_start: 0.6445 (m-80) cc_final: 0.6125 (m-80) REVERT: B 430 LYS cc_start: 0.7522 (mtpt) cc_final: 0.6738 (pttt) REVERT: D 11 LYS cc_start: 0.5461 (OUTLIER) cc_final: 0.5167 (mtmt) REVERT: D 66 PHE cc_start: 0.6956 (t80) cc_final: 0.6527 (t80) outliers start: 32 outliers final: 9 residues processed: 174 average time/residue: 0.4694 time to fit residues: 90.2407 Evaluate side-chains 135 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 142 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN D 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112058 restraints weight = 13332.348| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.36 r_work: 0.3146 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11310 Z= 0.212 Angle : 0.760 13.922 15453 Z= 0.363 Chirality : 0.048 0.329 1844 Planarity : 0.005 0.069 1850 Dihedral : 10.982 103.506 2174 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.19 % Allowed : 12.39 % Favored : 83.42 % 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: -0.58 (0.23), residues: 1325 helix: 0.84 (0.19), residues: 725 sheet: -1.07 (0.46), residues: 122 loop : -2.14 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 232 TYR 0.025 0.002 TYR C 218 PHE 0.043 0.003 PHE A 302 TRP 0.025 0.002 TRP A 640 HIS 0.013 0.002 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00516 (11284) covalent geometry : angle 0.73557 (15380) SS BOND : bond 0.00258 ( 5) SS BOND : angle 0.95168 ( 10) hydrogen bonds : bond 0.05370 ( 580) hydrogen bonds : angle 4.40656 ( 1680) link_BETA1-3 : bond 0.01058 ( 1) link_BETA1-3 : angle 1.27405 ( 3) link_BETA1-4 : bond 0.00506 ( 7) link_BETA1-4 : angle 2.12065 ( 21) link_BETA1-6 : bond 0.01926 ( 1) link_BETA1-6 : angle 3.50647 ( 3) link_NAG-ASN : bond 0.00669 ( 12) link_NAG-ASN : angle 3.58745 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8267 (mmmm) cc_final: 0.7899 (mmtm) REVERT: A 118 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8378 (mm) REVERT: A 184 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: A 364 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: A 395 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7399 (mm-30) REVERT: A 403 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7674 (tttm) REVERT: A 434 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7722 (tmm160) REVERT: A 655 ASP cc_start: 0.6805 (t0) cc_final: 0.6564 (t70) REVERT: A 666 LYS cc_start: 0.7289 (tptt) cc_final: 0.6589 (ttpp) REVERT: B 84 MET cc_start: 0.8500 (mtp) cc_final: 0.8283 (mtt) REVERT: B 270 MET cc_start: 0.7497 (mtp) cc_final: 0.7204 (mtp) REVERT: B 383 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 430 LYS cc_start: 0.7642 (mtpt) cc_final: 0.7386 (mtmm) REVERT: C 167 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7964 (mp) REVERT: D 11 LYS cc_start: 0.6048 (mtmp) cc_final: 0.5841 (mtmp) REVERT: D 33 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8513 (t0) outliers start: 48 outliers final: 19 residues processed: 160 average time/residue: 0.4757 time to fit residues: 83.9244 Evaluate side-chains 133 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114243 restraints weight = 13367.859| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.37 r_work: 0.3173 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11310 Z= 0.130 Angle : 0.630 12.515 15453 Z= 0.299 Chirality : 0.043 0.240 1844 Planarity : 0.004 0.054 1850 Dihedral : 10.307 97.196 2172 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.58 % Allowed : 14.22 % Favored : 82.20 % 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: -0.01 (0.23), residues: 1325 helix: 1.33 (0.20), residues: 725 sheet: -0.95 (0.46), residues: 120 loop : -1.88 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 539 TYR 0.016 0.001 TYR A 569 PHE 0.032 0.002 PHE A 302 TRP 0.015 0.001 TRP D 74 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00297 (11284) covalent geometry : angle 0.60993 (15380) SS BOND : bond 0.00235 ( 5) SS BOND : angle 0.74565 ( 10) hydrogen bonds : bond 0.04211 ( 580) hydrogen bonds : angle 4.18416 ( 1680) link_BETA1-3 : bond 0.00716 ( 1) link_BETA1-3 : angle 1.78587 ( 3) link_BETA1-4 : bond 0.00415 ( 7) link_BETA1-4 : angle 1.94207 ( 21) link_BETA1-6 : bond 0.01540 ( 1) link_BETA1-6 : angle 3.40848 ( 3) link_NAG-ASN : bond 0.00653 ( 12) link_NAG-ASN : angle 2.76030 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 53 LYS cc_start: 0.8285 (tppt) cc_final: 0.7787 (tptm) REVERT: A 46 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7759 (mmtm) REVERT: A 150 ASN cc_start: 0.8286 (p0) cc_final: 0.7826 (m-40) REVERT: A 395 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 403 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7720 (tttm) REVERT: A 434 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7775 (tmm160) REVERT: A 582 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6665 (p) REVERT: B 84 MET cc_start: 0.8418 (mtp) cc_final: 0.8218 (mtp) REVERT: B 270 MET cc_start: 0.7347 (mtp) cc_final: 0.7001 (mtp) REVERT: D 91 TYR cc_start: 0.8395 (m-80) cc_final: 0.7993 (m-80) outliers start: 41 outliers final: 15 residues processed: 140 average time/residue: 0.4910 time to fit residues: 75.8560 Evaluate side-chains 116 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 420 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122095 restraints weight = 13033.242| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.25 r_work: 0.3349 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11310 Z= 0.156 Angle : 0.648 12.829 15453 Z= 0.309 Chirality : 0.044 0.260 1844 Planarity : 0.004 0.044 1850 Dihedral : 9.657 75.673 2172 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.19 % Allowed : 14.83 % Favored : 80.98 % 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: 0.25 (0.24), residues: 1325 helix: 1.56 (0.20), residues: 725 sheet: -0.78 (0.45), residues: 126 loop : -1.82 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 371 TYR 0.017 0.002 TYR A 337 PHE 0.033 0.002 PHE A 302 TRP 0.014 0.001 TRP D 74 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00375 (11284) covalent geometry : angle 0.63065 (15380) SS BOND : bond 0.00266 ( 5) SS BOND : angle 0.77135 ( 10) hydrogen bonds : bond 0.04369 ( 580) hydrogen bonds : angle 4.06790 ( 1680) link_BETA1-3 : bond 0.00824 ( 1) link_BETA1-3 : angle 1.82833 ( 3) link_BETA1-4 : bond 0.00437 ( 7) link_BETA1-4 : angle 1.75607 ( 21) link_BETA1-6 : bond 0.01261 ( 1) link_BETA1-6 : angle 3.37557 ( 3) link_NAG-ASN : bond 0.00430 ( 12) link_NAG-ASN : angle 2.67574 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8272 (mmmm) cc_final: 0.7983 (mmtm) REVERT: A 150 ASN cc_start: 0.8317 (p0) cc_final: 0.7969 (m-40) REVERT: A 184 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: A 374 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7316 (mt) REVERT: A 395 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7361 (mm-30) REVERT: A 403 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7712 (tttm) REVERT: A 582 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7175 (p) REVERT: B 270 MET cc_start: 0.7267 (mtp) cc_final: 0.6847 (mtp) REVERT: C 146 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8164 (m) REVERT: D 11 LYS cc_start: 0.6121 (mtmp) cc_final: 0.5918 (mtmp) outliers start: 48 outliers final: 22 residues processed: 146 average time/residue: 0.4844 time to fit residues: 78.1742 Evaluate side-chains 128 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 35 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121090 restraints weight = 13155.215| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.25 r_work: 0.3336 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11310 Z= 0.172 Angle : 0.655 12.388 15453 Z= 0.312 Chirality : 0.044 0.243 1844 Planarity : 0.004 0.044 1850 Dihedral : 9.432 75.294 2172 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.75 % Allowed : 15.53 % Favored : 80.72 % 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: 0.34 (0.24), residues: 1325 helix: 1.62 (0.20), residues: 726 sheet: -0.65 (0.46), residues: 126 loop : -1.80 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 62 TYR 0.016 0.002 TYR A 569 PHE 0.033 0.002 PHE A 302 TRP 0.010 0.001 TRP A 84 HIS 0.008 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00418 (11284) covalent geometry : angle 0.63775 (15380) SS BOND : bond 0.00257 ( 5) SS BOND : angle 0.72370 ( 10) hydrogen bonds : bond 0.04395 ( 580) hydrogen bonds : angle 4.07449 ( 1680) link_BETA1-3 : bond 0.00800 ( 1) link_BETA1-3 : angle 1.53420 ( 3) link_BETA1-4 : bond 0.00315 ( 7) link_BETA1-4 : angle 1.77676 ( 21) link_BETA1-6 : bond 0.00824 ( 1) link_BETA1-6 : angle 3.53364 ( 3) link_NAG-ASN : bond 0.00531 ( 12) link_NAG-ASN : angle 2.69001 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8329 (mmmm) cc_final: 0.8025 (mmtm) REVERT: A 150 ASN cc_start: 0.8321 (p0) cc_final: 0.8014 (m-40) REVERT: A 184 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: A 364 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: A 374 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7297 (mt) REVERT: A 395 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7398 (tp30) REVERT: A 403 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7649 (tttm) REVERT: A 582 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7325 (p) REVERT: A 603 SER cc_start: 0.8037 (p) cc_final: 0.7836 (t) REVERT: B 270 MET cc_start: 0.7324 (mtp) cc_final: 0.6966 (mtp) REVERT: B 430 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7376 (mtmm) REVERT: C 146 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8163 (m) REVERT: D 91 TYR cc_start: 0.8648 (m-80) cc_final: 0.8339 (m-80) outliers start: 43 outliers final: 26 residues processed: 142 average time/residue: 0.5186 time to fit residues: 80.9406 Evaluate side-chains 135 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120498 restraints weight = 13185.248| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.22 r_work: 0.3304 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11310 Z= 0.221 Angle : 0.707 12.415 15453 Z= 0.337 Chirality : 0.046 0.240 1844 Planarity : 0.004 0.041 1850 Dihedral : 9.502 74.203 2172 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.10 % Allowed : 15.71 % Favored : 80.19 % 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: 0.14 (0.24), residues: 1325 helix: 1.42 (0.20), residues: 732 sheet: -0.66 (0.46), residues: 126 loop : -1.89 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 543 TYR 0.018 0.002 TYR A 337 PHE 0.036 0.002 PHE A 302 TRP 0.013 0.002 TRP A 257 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00548 (11284) covalent geometry : angle 0.68654 (15380) SS BOND : bond 0.00291 ( 5) SS BOND : angle 0.84585 ( 10) hydrogen bonds : bond 0.04945 ( 580) hydrogen bonds : angle 4.17985 ( 1680) link_BETA1-3 : bond 0.00815 ( 1) link_BETA1-3 : angle 1.54551 ( 3) link_BETA1-4 : bond 0.00372 ( 7) link_BETA1-4 : angle 1.80823 ( 21) link_BETA1-6 : bond 0.01054 ( 1) link_BETA1-6 : angle 3.50094 ( 3) link_NAG-ASN : bond 0.00668 ( 12) link_NAG-ASN : angle 3.10712 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8212 (mmtm) REVERT: A 150 ASN cc_start: 0.8324 (p0) cc_final: 0.8113 (m-40) REVERT: A 184 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: A 364 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: A 374 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7445 (mt) REVERT: A 395 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7518 (tp30) REVERT: A 403 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7930 (ttpp) REVERT: A 582 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7588 (p) REVERT: B 210 MET cc_start: 0.8641 (mmt) cc_final: 0.8333 (mmm) REVERT: B 270 MET cc_start: 0.7578 (mtp) cc_final: 0.7218 (mtp) REVERT: B 430 LYS cc_start: 0.7783 (mtpt) cc_final: 0.7491 (mtmm) REVERT: C 146 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8235 (m) REVERT: D 59 ARG cc_start: 0.7876 (ttm170) cc_final: 0.7640 (mtt90) REVERT: D 91 TYR cc_start: 0.8798 (m-80) cc_final: 0.8516 (m-80) outliers start: 47 outliers final: 27 residues processed: 139 average time/residue: 0.5185 time to fit residues: 79.0521 Evaluate side-chains 128 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 0.4980 chunk 81 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123660 restraints weight = 13006.087| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.25 r_work: 0.3368 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11310 Z= 0.115 Angle : 0.608 11.814 15453 Z= 0.289 Chirality : 0.042 0.228 1844 Planarity : 0.004 0.038 1850 Dihedral : 8.969 74.467 2172 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.06 % Rotamer: Outliers : 2.97 % Allowed : 16.84 % Favored : 80.19 % 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: 0.59 (0.24), residues: 1325 helix: 1.82 (0.20), residues: 725 sheet: -0.50 (0.47), residues: 124 loop : -1.69 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 543 TYR 0.015 0.001 TYR A 569 PHE 0.029 0.001 PHE A 302 TRP 0.010 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00250 (11284) covalent geometry : angle 0.58885 (15380) SS BOND : bond 0.00156 ( 5) SS BOND : angle 0.57172 ( 10) hydrogen bonds : bond 0.03713 ( 580) hydrogen bonds : angle 4.02430 ( 1680) link_BETA1-3 : bond 0.01021 ( 1) link_BETA1-3 : angle 1.60924 ( 3) link_BETA1-4 : bond 0.00512 ( 7) link_BETA1-4 : angle 1.57732 ( 21) link_BETA1-6 : bond 0.00970 ( 1) link_BETA1-6 : angle 3.19664 ( 3) link_NAG-ASN : bond 0.00942 ( 12) link_NAG-ASN : angle 2.85241 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8042 (mmtm) REVERT: A 184 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: A 253 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8408 (t70) REVERT: A 283 ASP cc_start: 0.8997 (p0) cc_final: 0.8706 (p0) REVERT: A 395 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7401 (tp30) REVERT: A 403 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7820 (ttpp) REVERT: A 508 SER cc_start: 0.8083 (p) cc_final: 0.7857 (t) REVERT: A 582 THR cc_start: 0.7771 (OUTLIER) cc_final: 0.7456 (p) REVERT: B 210 MET cc_start: 0.8523 (mmt) cc_final: 0.8166 (mmm) REVERT: B 270 MET cc_start: 0.7398 (mtp) cc_final: 0.7084 (mtp) REVERT: D 91 TYR cc_start: 0.8652 (m-80) cc_final: 0.8338 (m-80) outliers start: 34 outliers final: 15 residues processed: 133 average time/residue: 0.4827 time to fit residues: 71.1204 Evaluate side-chains 120 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 112 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.153831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119267 restraints weight = 12949.999| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.19 r_work: 0.3301 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11310 Z= 0.226 Angle : 0.730 21.217 15453 Z= 0.342 Chirality : 0.051 0.942 1844 Planarity : 0.004 0.043 1850 Dihedral : 9.109 73.684 2172 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 2.97 % Allowed : 17.10 % Favored : 79.93 % 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: 0.28 (0.24), residues: 1325 helix: 1.52 (0.20), residues: 733 sheet: -0.53 (0.46), residues: 128 loop : -1.83 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 543 TYR 0.018 0.002 TYR A 337 PHE 0.035 0.002 PHE A 302 TRP 0.011 0.002 TRP D 36 HIS 0.009 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00561 (11284) covalent geometry : angle 0.68060 (15380) SS BOND : bond 0.00294 ( 5) SS BOND : angle 0.79735 ( 10) hydrogen bonds : bond 0.04792 ( 580) hydrogen bonds : angle 4.15065 ( 1680) link_BETA1-3 : bond 0.00857 ( 1) link_BETA1-3 : angle 1.57901 ( 3) link_BETA1-4 : bond 0.00424 ( 7) link_BETA1-4 : angle 1.73513 ( 21) link_BETA1-6 : bond 0.00909 ( 1) link_BETA1-6 : angle 3.17997 ( 3) link_NAG-ASN : bond 0.00903 ( 12) link_NAG-ASN : angle 5.26712 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: E 49 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8245 (mt) REVERT: A 46 LYS cc_start: 0.8505 (mmmm) cc_final: 0.8208 (mmtm) REVERT: A 184 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: A 364 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: A 403 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7955 (ttpp) REVERT: A 582 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7635 (p) REVERT: A 588 ASP cc_start: 0.7623 (t0) cc_final: 0.7171 (OUTLIER) REVERT: B 210 MET cc_start: 0.8659 (mmt) cc_final: 0.8388 (mmm) REVERT: B 270 MET cc_start: 0.7572 (mtp) cc_final: 0.7188 (mtp) REVERT: B 430 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7526 (mtmm) REVERT: B 435 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7799 (mp) REVERT: D 91 TYR cc_start: 0.8788 (m-80) cc_final: 0.8525 (m-80) outliers start: 34 outliers final: 22 residues processed: 124 average time/residue: 0.5428 time to fit residues: 73.8530 Evaluate side-chains 120 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 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 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124978 restraints weight = 13033.688| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.22 r_work: 0.3380 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11310 Z= 0.117 Angle : 0.633 19.951 15453 Z= 0.292 Chirality : 0.044 0.519 1844 Planarity : 0.004 0.041 1850 Dihedral : 8.614 74.078 2172 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 2.27 % Allowed : 17.71 % Favored : 80.02 % 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: 0.63 (0.24), residues: 1325 helix: 1.84 (0.20), residues: 727 sheet: -0.40 (0.47), residues: 124 loop : -1.69 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 543 TYR 0.014 0.001 TYR A 569 PHE 0.030 0.001 PHE A 302 TRP 0.012 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00258 (11284) covalent geometry : angle 0.58696 (15380) SS BOND : bond 0.00140 ( 5) SS BOND : angle 0.52610 ( 10) hydrogen bonds : bond 0.03622 ( 580) hydrogen bonds : angle 4.00166 ( 1680) link_BETA1-3 : bond 0.00824 ( 1) link_BETA1-3 : angle 1.48624 ( 3) link_BETA1-4 : bond 0.00367 ( 7) link_BETA1-4 : angle 1.51168 ( 21) link_BETA1-6 : bond 0.00903 ( 1) link_BETA1-6 : angle 2.51912 ( 3) link_NAG-ASN : bond 0.01349 ( 12) link_NAG-ASN : angle 4.76628 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8397 (mmmm) cc_final: 0.7975 (mmtm) REVERT: A 184 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: A 403 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7903 (ttpp) REVERT: A 582 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7679 (p) REVERT: A 588 ASP cc_start: 0.7539 (t0) cc_final: 0.7160 (OUTLIER) REVERT: A 662 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8749 (mp) REVERT: B 145 VAL cc_start: 0.7903 (p) cc_final: 0.7513 (m) REVERT: B 210 MET cc_start: 0.8536 (mmt) cc_final: 0.8214 (mmm) REVERT: B 270 MET cc_start: 0.7450 (mtp) cc_final: 0.7081 (mtp) REVERT: B 435 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7607 (mp) REVERT: D 11 LYS cc_start: 0.6591 (mtmm) cc_final: 0.6330 (mtmm) REVERT: D 12 LEU cc_start: 0.7464 (tm) cc_final: 0.7257 (tp) REVERT: D 91 TYR cc_start: 0.8621 (m-80) cc_final: 0.8332 (m-80) outliers start: 26 outliers final: 19 residues processed: 120 average time/residue: 0.4721 time to fit residues: 62.9503 Evaluate side-chains 116 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117462 restraints weight = 13077.311| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.26 r_work: 0.3335 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11310 Z= 0.165 Angle : 0.673 20.647 15453 Z= 0.313 Chirality : 0.045 0.495 1844 Planarity : 0.004 0.042 1850 Dihedral : 8.598 73.491 2172 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 3.05 % Allowed : 17.19 % Favored : 79.76 % 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: 1325 helix: 1.76 (0.20), residues: 728 sheet: -0.50 (0.46), residues: 126 loop : -1.66 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 543 TYR 0.016 0.001 TYR A 569 PHE 0.031 0.002 PHE A 302 TRP 0.009 0.001 TRP A 257 HIS 0.007 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00398 (11284) covalent geometry : angle 0.62689 (15380) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.66844 ( 10) hydrogen bonds : bond 0.04230 ( 580) hydrogen bonds : angle 4.03669 ( 1680) link_BETA1-3 : bond 0.00771 ( 1) link_BETA1-3 : angle 1.60866 ( 3) link_BETA1-4 : bond 0.00325 ( 7) link_BETA1-4 : angle 1.60382 ( 21) link_BETA1-6 : bond 0.00811 ( 1) link_BETA1-6 : angle 2.31277 ( 3) link_NAG-ASN : bond 0.01076 ( 12) link_NAG-ASN : angle 4.92019 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3739.97 seconds wall clock time: 64 minutes 46.97 seconds (3886.97 seconds total)