Starting phenix.real_space_refine on Fri Jan 17 15:46:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x54_38061/01_2025/8x54_38061.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x54_38061/01_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_38061/01_2025/8x54_38061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x54_38061/01_2025/8x54_38061.map" model { file = "/net/cci-nas-00/data/ceres_data/8x54_38061/01_2025/8x54_38061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x54_38061/01_2025/8x54_38061.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 6.80, per 1000 atoms: 0.62 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: 3.23 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.16 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: 3.61 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 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: 0.330 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: 0.360 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 27.950 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- 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 : 0.010 0.184 11284 Z= 0.593 Angle : 1.149 28.667 15380 Z= 0.682 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (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 TRP 0.053 0.004 TRP C 227 HIS 0.024 0.003 HIS C 197 PHE 0.040 0.003 PHE B 386 TYR 0.035 0.003 TYR A 565 ARG 0.009 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 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 : 1.126 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: 1.0007 time to fit residues: 271.3364 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 : 1.217 ------------------------------------------------------------------------------- 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 110 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.164984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130154 restraints weight = 13152.162| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.35 r_work: 0.3400 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11284 Z= 0.164 Angle : 0.637 12.214 15380 Z= 0.314 Chirality : 0.044 0.357 1844 Planarity : 0.005 0.041 1850 Dihedral : 12.917 103.123 2180 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.71 % Allowed : 10.91 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.22), residues: 1325 helix: 0.34 (0.19), residues: 724 sheet: -1.04 (0.49), residues: 108 loop : -2.41 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 227 HIS 0.008 0.001 HIS C 197 PHE 0.035 0.002 PHE A 302 TYR 0.015 0.001 TYR A 569 ARG 0.003 0.000 ARG A 160 *********************** 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 189 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.121 Fit side-chains REVERT: A 46 LYS cc_start: 0.8188 (mmmm) cc_final: 0.7882 (mmtm) REVERT: A 78 LYS cc_start: 0.7443 (ptpt) cc_final: 0.7121 (pttm) REVERT: A 235 SER cc_start: 0.7483 (t) cc_final: 0.7190 (p) REVERT: A 364 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: A 395 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7358 (mm-30) REVERT: A 528 LYS cc_start: 0.8203 (tttt) cc_final: 0.7905 (tttm) REVERT: B 180 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8165 (mm) REVERT: B 283 PHE cc_start: 0.6416 (m-80) cc_final: 0.6037 (m-80) REVERT: B 430 LYS cc_start: 0.7494 (mtpt) cc_final: 0.6727 (pttt) REVERT: C 167 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7798 (mp) REVERT: D 11 LYS cc_start: 0.5449 (OUTLIER) cc_final: 0.5151 (mtmt) REVERT: D 66 PHE cc_start: 0.6949 (t80) cc_final: 0.6531 (t80) outliers start: 31 outliers final: 7 residues processed: 175 average time/residue: 0.9967 time to fit residues: 192.2057 Evaluate side-chains 132 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 167 ILE 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 80 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 68 optimal weight: 0.1980 chunk 56 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN D 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124680 restraints weight = 13271.200| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.36 r_work: 0.3332 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11284 Z= 0.165 Angle : 0.594 12.588 15380 Z= 0.287 Chirality : 0.043 0.288 1844 Planarity : 0.004 0.037 1850 Dihedral : 10.742 109.212 2174 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.23 % Allowed : 13.18 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1325 helix: 1.20 (0.20), residues: 719 sheet: -0.70 (0.50), residues: 108 loop : -1.99 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.034 0.002 PHE A 302 TYR 0.014 0.001 TYR A 565 ARG 0.004 0.000 ARG A 543 *********************** 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 170 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8241 (mmmm) cc_final: 0.7832 (mmtm) REVERT: A 184 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: A 395 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7327 (mm-30) REVERT: A 396 ASP cc_start: 0.7467 (m-30) cc_final: 0.7237 (m-30) REVERT: A 403 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7577 (tttm) REVERT: A 434 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7265 (tmm160) REVERT: B 180 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8421 (mm) REVERT: B 258 LEU cc_start: 0.8490 (tp) cc_final: 0.8269 (tp) REVERT: B 270 MET cc_start: 0.7209 (mtp) cc_final: 0.6970 (mtp) REVERT: B 283 PHE cc_start: 0.6314 (m-80) cc_final: 0.6082 (m-80) REVERT: C 62 ARG cc_start: 0.6621 (tmm160) cc_final: 0.6346 (tmm160) REVERT: C 184 ARG cc_start: 0.7564 (mtp180) cc_final: 0.7345 (mmm-85) REVERT: D 66 PHE cc_start: 0.7447 (t80) cc_final: 0.6904 (t80) outliers start: 37 outliers final: 12 residues processed: 159 average time/residue: 0.9406 time to fit residues: 165.4776 Evaluate side-chains 131 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 A residue 184 GLU Chi-restraints excluded: chain A residue 258 SER 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 B residue 180 ILE Chi-restraints excluded: chain B residue 248 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 1 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 14 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN 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 = 0.3737 r_free = 0.3737 target = 0.150185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113772 restraints weight = 13084.627| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.34 r_work: 0.3197 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11284 Z= 0.261 Angle : 0.669 12.393 15380 Z= 0.324 Chirality : 0.045 0.243 1844 Planarity : 0.004 0.065 1850 Dihedral : 10.128 95.521 2172 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.32 % Allowed : 14.40 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1325 helix: 1.42 (0.20), residues: 718 sheet: -1.07 (0.43), residues: 130 loop : -2.00 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 640 HIS 0.010 0.002 HIS C 197 PHE 0.037 0.002 PHE A 302 TYR 0.020 0.002 TYR C 218 ARG 0.006 0.001 ARG A 342 *********************** 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 156 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.268 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.8011 (tptt) cc_final: 0.7362 (tptm) REVERT: A 46 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7872 (mmtm) REVERT: A 150 ASN cc_start: 0.8292 (p0) cc_final: 0.7843 (m-40) REVERT: A 364 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: A 395 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7406 (mm-30) REVERT: A 396 ASP cc_start: 0.7461 (m-30) cc_final: 0.7217 (m-30) REVERT: A 403 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7614 (tttm) REVERT: A 434 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7719 (tmm160) REVERT: A 528 LYS cc_start: 0.8591 (tttt) cc_final: 0.8247 (tttm) REVERT: A 582 THR cc_start: 0.6973 (OUTLIER) cc_final: 0.6594 (p) REVERT: B 210 MET cc_start: 0.8513 (mmp) cc_final: 0.8296 (mmm) REVERT: B 270 MET cc_start: 0.7002 (mtp) cc_final: 0.6708 (mtp) REVERT: C 62 ARG cc_start: 0.6660 (tmm160) cc_final: 0.6285 (tmm160) REVERT: D 33 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8347 (t0) REVERT: D 91 TYR cc_start: 0.8107 (m-80) cc_final: 0.7621 (m-80) outliers start: 38 outliers final: 15 residues processed: 144 average time/residue: 0.9655 time to fit residues: 153.9311 Evaluate side-chains 125 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 235 SER 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 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 580 ASN Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 422 LEU 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 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** D 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115637 restraints weight = 13168.077| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.33 r_work: 0.3218 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11284 Z= 0.173 Angle : 0.584 12.423 15380 Z= 0.283 Chirality : 0.042 0.244 1844 Planarity : 0.004 0.056 1850 Dihedral : 9.680 81.816 2172 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.97 % Allowed : 15.97 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1325 helix: 1.67 (0.20), residues: 724 sheet: -1.04 (0.43), residues: 132 loop : -1.78 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 74 HIS 0.006 0.001 HIS C 197 PHE 0.030 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.002 0.000 ARG A 543 *********************** 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 145 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8217 (mp) REVERT: E 53 LYS cc_start: 0.8043 (tptt) cc_final: 0.7343 (tptm) REVERT: A 46 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7787 (mmtm) REVERT: A 150 ASN cc_start: 0.8250 (p0) cc_final: 0.7852 (m-40) REVERT: A 184 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: A 395 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7399 (mm-30) REVERT: A 403 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7618 (tttm) REVERT: A 434 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7692 (tmm160) REVERT: B 210 MET cc_start: 0.8528 (mmp) cc_final: 0.8268 (mmm) REVERT: B 270 MET cc_start: 0.7165 (mtp) cc_final: 0.6834 (mtp) REVERT: C 62 ARG cc_start: 0.6575 (tmm160) cc_final: 0.6218 (tmm160) REVERT: C 117 MET cc_start: 0.8606 (mtp) cc_final: 0.8280 (mtt) REVERT: D 54 LYS cc_start: 0.6079 (ttpt) cc_final: 0.5860 (ttpp) REVERT: D 91 TYR cc_start: 0.8112 (m-80) cc_final: 0.7650 (m-80) outliers start: 34 outliers final: 19 residues processed: 136 average time/residue: 0.9378 time to fit residues: 141.9338 Evaluate side-chains 123 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 49 LEU Chi-restraints excluded: chain E residue 50 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 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 605 VAL Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain D residue 65 LEU 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 125 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** 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 = 0.3862 r_free = 0.3862 target = 0.154098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118966 restraints weight = 13157.817| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.25 r_work: 0.3303 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 11284 Z= 0.432 Angle : 0.733 13.007 15380 Z= 0.356 Chirality : 0.048 0.272 1844 Planarity : 0.005 0.059 1850 Dihedral : 9.771 75.281 2172 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.45 % Allowed : 15.01 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.23), residues: 1325 helix: 1.29 (0.20), residues: 732 sheet: -0.97 (0.44), residues: 130 loop : -1.93 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 227 HIS 0.013 0.002 HIS C 197 PHE 0.040 0.003 PHE A 302 TYR 0.021 0.002 TYR C 218 ARG 0.009 0.001 ARG A 657 *********************** 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 161 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 110 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: E 49 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8219 (mt) REVERT: E 53 LYS cc_start: 0.8077 (tptt) cc_final: 0.7411 (tptm) REVERT: A 46 LYS cc_start: 0.8288 (mmmm) cc_final: 0.8031 (mmtm) REVERT: A 114 ARG cc_start: 0.7294 (mtt-85) cc_final: 0.7058 (mtp85) REVERT: A 150 ASN cc_start: 0.8348 (p0) cc_final: 0.8004 (m-40) REVERT: A 184 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: A 231 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8238 (mmm) REVERT: A 364 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: A 374 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7299 (mt) REVERT: A 395 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7402 (mm-30) REVERT: A 403 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7616 (tttm) REVERT: A 434 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7763 (tmm160) REVERT: A 582 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7245 (p) REVERT: B 270 MET cc_start: 0.7320 (mtp) cc_final: 0.7018 (mtp) REVERT: B 430 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7487 (mtmm) REVERT: B 435 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7742 (mp) REVERT: C 146 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8232 (m) REVERT: D 54 LYS cc_start: 0.6489 (ttpt) cc_final: 0.6284 (ttpp) REVERT: D 91 TYR cc_start: 0.8287 (m-80) cc_final: 0.8040 (m-80) outliers start: 51 outliers final: 26 residues processed: 146 average time/residue: 1.0202 time to fit residues: 164.2961 Evaluate side-chains 138 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 49 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 235 SER 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 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 A residue 655 ASP Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 416 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 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 68 VAL Chi-restraints excluded: chain D residue 77 ILE 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 10 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113804 restraints weight = 13304.307| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.35 r_work: 0.3197 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11284 Z= 0.162 Angle : 0.589 12.449 15380 Z= 0.283 Chirality : 0.042 0.244 1844 Planarity : 0.004 0.044 1850 Dihedral : 9.273 75.991 2172 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.64 % Favored : 97.28 % Rotamer: Outliers : 2.79 % Allowed : 17.36 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1325 helix: 1.69 (0.20), residues: 732 sheet: -0.70 (0.45), residues: 126 loop : -1.74 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 74 HIS 0.005 0.001 HIS C 197 PHE 0.029 0.001 PHE A 302 TYR 0.015 0.001 TYR A 569 ARG 0.011 0.000 ARG D 59 *********************** 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 138 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8168 (mmmm) cc_final: 0.7764 (mmtm) REVERT: A 150 ASN cc_start: 0.8256 (p0) cc_final: 0.7959 (m-40) REVERT: A 253 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8509 (t70) REVERT: A 374 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7076 (mt) REVERT: A 395 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7368 (tp30) REVERT: A 403 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7642 (tttm) REVERT: A 434 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7810 (tmm160) REVERT: A 582 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7377 (p) REVERT: B 210 MET cc_start: 0.8514 (mmp) cc_final: 0.8236 (mmm) REVERT: B 270 MET cc_start: 0.7217 (mtp) cc_final: 0.6942 (mtp) REVERT: B 435 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7665 (mp) REVERT: C 90 TYR cc_start: 0.8975 (t80) cc_final: 0.8770 (t80) REVERT: C 117 MET cc_start: 0.8566 (mtp) cc_final: 0.8251 (mtt) REVERT: D 54 LYS cc_start: 0.6588 (ttpt) cc_final: 0.6362 (ttpp) REVERT: D 91 TYR cc_start: 0.8245 (m-80) cc_final: 0.7933 (m-80) outliers start: 32 outliers final: 16 residues processed: 129 average time/residue: 1.0076 time to fit residues: 143.9444 Evaluate side-chains 124 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 238 SER Chi-restraints excluded: chain A residue 253 ASP 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 378 MET Chi-restraints excluded: chain A residue 393 GLN 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 435 LEU Chi-restraints excluded: chain C residue 57 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 84 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.150167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114157 restraints weight = 13171.842| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.35 r_work: 0.3181 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11284 Z= 0.161 Angle : 0.584 12.234 15380 Z= 0.280 Chirality : 0.046 0.820 1844 Planarity : 0.004 0.044 1850 Dihedral : 8.991 75.021 2172 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 2.71 % Allowed : 17.71 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1325 helix: 1.88 (0.20), residues: 728 sheet: -0.60 (0.46), residues: 126 loop : -1.61 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 74 HIS 0.004 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.008 0.000 ARG D 59 *********************** 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 136 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8166 (mmmm) cc_final: 0.7769 (mmtm) REVERT: A 150 ASN cc_start: 0.8248 (p0) cc_final: 0.8024 (m-40) REVERT: A 283 ASP cc_start: 0.8890 (p0) cc_final: 0.8639 (p0) REVERT: A 364 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: A 395 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7426 (tp30) REVERT: A 403 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7653 (tttm) REVERT: A 434 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7824 (tmm160) REVERT: A 582 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7354 (p) REVERT: B 270 MET cc_start: 0.7141 (mtp) cc_final: 0.6811 (mtp) REVERT: B 435 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7499 (mp) REVERT: D 54 LYS cc_start: 0.6545 (ttpt) cc_final: 0.6333 (ttpp) REVERT: D 91 TYR cc_start: 0.8234 (m-80) cc_final: 0.7907 (m-80) outliers start: 31 outliers final: 17 residues processed: 128 average time/residue: 1.0321 time to fit residues: 145.5277 Evaluate side-chains 127 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 378 MET Chi-restraints excluded: chain A residue 393 GLN 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 561 THR Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 57 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.149433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113769 restraints weight = 13258.521| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.34 r_work: 0.3180 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11284 Z= 0.204 Angle : 0.610 12.021 15380 Z= 0.293 Chirality : 0.044 0.506 1844 Planarity : 0.004 0.043 1850 Dihedral : 8.791 74.690 2172 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 2.62 % Allowed : 17.80 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1325 helix: 1.89 (0.20), residues: 727 sheet: -0.54 (0.46), residues: 126 loop : -1.61 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.001 PHE A 302 TYR 0.015 0.001 TYR A 569 ARG 0.008 0.000 ARG D 59 *********************** 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 134 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7762 (mmtm) REVERT: A 364 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: A 395 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7478 (tp30) REVERT: A 403 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7637 (tttm) REVERT: A 582 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7395 (p) REVERT: B 270 MET cc_start: 0.7130 (mtp) cc_final: 0.6777 (mtp) REVERT: B 435 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7684 (mp) REVERT: D 91 TYR cc_start: 0.8286 (m-80) cc_final: 0.7961 (m-80) outliers start: 30 outliers final: 20 residues processed: 125 average time/residue: 1.0762 time to fit residues: 149.8486 Evaluate side-chains 124 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 378 MET 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 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 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 77 ILE 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 117 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.151840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116287 restraints weight = 13159.091| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.35 r_work: 0.3221 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11284 Z= 0.153 Angle : 0.568 11.205 15380 Z= 0.273 Chirality : 0.043 0.472 1844 Planarity : 0.004 0.038 1850 Dihedral : 8.369 74.529 2172 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.91 % Rotamer: Outliers : 2.01 % Allowed : 18.50 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1325 helix: 2.04 (0.20), residues: 728 sheet: -0.40 (0.46), residues: 124 loop : -1.51 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 36 HIS 0.004 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.008 0.000 ARG A 543 ********************** 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 131 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 51 MET cc_start: 0.8781 (ttm) cc_final: 0.8334 (ttp) REVERT: A 46 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7742 (mmtm) REVERT: A 266 THR cc_start: 0.8112 (m) cc_final: 0.7868 (p) REVERT: A 283 ASP cc_start: 0.8884 (p0) cc_final: 0.8642 (p0) REVERT: A 364 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: A 395 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7446 (tp30) REVERT: A 403 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7799 (ttpp) REVERT: A 508 SER cc_start: 0.7916 (p) cc_final: 0.7703 (t) REVERT: A 582 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7397 (p) REVERT: B 145 VAL cc_start: 0.7736 (p) cc_final: 0.7340 (m) REVERT: B 270 MET cc_start: 0.7126 (mtp) cc_final: 0.6771 (mtp) REVERT: B 435 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7443 (mp) REVERT: C 117 MET cc_start: 0.8452 (mtp) cc_final: 0.8141 (mtt) REVERT: C 167 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7820 (mp) REVERT: D 91 TYR cc_start: 0.8231 (m-80) cc_final: 0.7850 (m-80) outliers start: 23 outliers final: 16 residues processed: 124 average time/residue: 1.0532 time to fit residues: 144.2585 Evaluate side-chains 123 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 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 B residue 169 SER 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 167 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN A 420 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113337 restraints weight = 13128.184| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.32 r_work: 0.3162 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11284 Z= 0.223 Angle : 0.607 11.662 15380 Z= 0.294 Chirality : 0.044 0.479 1844 Planarity : 0.004 0.042 1850 Dihedral : 8.301 74.175 2172 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 2.62 % Allowed : 18.24 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1325 helix: 1.94 (0.20), residues: 728 sheet: -0.50 (0.46), residues: 126 loop : -1.57 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.001 PHE A 302 TYR 0.016 0.001 TYR A 569 ARG 0.008 0.000 ARG A 543 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7032.33 seconds wall clock time: 126 minutes 40.52 seconds (7600.52 seconds total)