Starting phenix.real_space_refine on Tue Jul 29 04:21:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x54_38061/07_2025/8x54_38061.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x54_38061/07_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_38061/07_2025/8x54_38061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x54_38061/07_2025/8x54_38061.map" model { file = "/net/cci-nas-00/data/ceres_data/8x54_38061/07_2025/8x54_38061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x54_38061/07_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-5711/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: 7.32, per 1000 atoms: 0.66 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: 3.24 Conformation dependent library (CDL) restraints added in 1.6 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: 1.24 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: 3.47 Time building geometry restraints manager: 3.76 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: 0.550 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.220 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.465 11310 Z= 0.904 Angle : 1.364 61.435 15453 Z= 0.724 Chirality : 0.068 0.670 1844 Planarity : 0.007 0.071 1850 Dihedral : 14.622 117.489 4519 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.05 % Allowed : 2.79 % Favored : 96.16 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd link_NAG-ASN : bond 0.42309 ( 12) link_NAG-ASN : angle 15.17694 ( 36) link_BETA1-4 : bond 0.00217 ( 7) link_BETA1-4 : angle 2.21426 ( 21) hydrogen bonds : bond 0.19362 ( 580) hydrogen bonds : angle 7.02869 ( 1680) link_BETA1-6 : bond 0.00496 ( 1) link_BETA1-6 : angle 1.46826 ( 3) SS BOND : bond 0.00641 ( 5) SS BOND : angle 2.15695 ( 10) link_BETA1-3 : bond 0.00002 ( 1) link_BETA1-3 : angle 1.60727 ( 3) covalent geometry : bond 0.00971 (11284) covalent geometry : angle 1.14922 (15380) *********************** 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 : 1.230 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: 1.1139 time to fit residues: 301.9834 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 : 1.716 ------------------------------------------------------------------------------- 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 = 0.130155 restraints weight = 13152.184| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.35 r_work: 0.3401 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- 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 11310 Z= 0.126 Angle : 0.662 12.214 15453 Z= 0.319 Chirality : 0.044 0.357 1844 Planarity : 0.005 0.041 1850 Dihedral : 12.917 103.121 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 12) link_NAG-ASN : angle 3.30711 ( 36) link_BETA1-4 : bond 0.00508 ( 7) link_BETA1-4 : angle 1.86757 ( 21) hydrogen bonds : bond 0.04810 ( 580) hydrogen bonds : angle 4.62756 ( 1680) link_BETA1-6 : bond 0.01488 ( 1) link_BETA1-6 : angle 3.11339 ( 3) SS BOND : bond 0.00631 ( 5) SS BOND : angle 1.10399 ( 10) link_BETA1-3 : bond 0.00798 ( 1) link_BETA1-3 : angle 2.24947 ( 3) covalent geometry : bond 0.00259 (11284) covalent geometry : angle 0.63726 (15380) *********************** 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 : 2.199 Fit side-chains REVERT: A 46 LYS cc_start: 0.8189 (mmmm) cc_final: 0.7882 (mmtm) REVERT: A 78 LYS cc_start: 0.7442 (ptpt) cc_final: 0.7122 (pttm) REVERT: A 235 SER cc_start: 0.7482 (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: 0.8414 (OUTLIER) cc_final: 0.8165 (mm) REVERT: B 283 PHE cc_start: 0.6415 (m-80) cc_final: 0.6036 (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: 0.5450 (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: 0.9674 time to fit residues: 187.2383 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 : 1.132 ------------------------------------------------------------------------------- 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: 0.4980 chunk 109 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 68 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 142 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114031 restraints weight = 13248.166| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.36 r_work: 0.3171 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11310 Z= 0.191 Angle : 0.731 13.581 15453 Z= 0.346 Chirality : 0.046 0.245 1844 Planarity : 0.004 0.037 1850 Dihedral : 10.757 105.936 2174 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.01 % Allowed : 12.74 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.23), residues: 1325 helix: 1.07 (0.19), residues: 719 sheet: -1.03 (0.46), residues: 122 loop : -2.02 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 640 HIS 0.010 0.002 HIS C 197 PHE 0.040 0.003 PHE A 302 TYR 0.023 0.002 TYR C 218 ARG 0.005 0.001 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.01039 ( 12) link_NAG-ASN : angle 3.70509 ( 36) link_BETA1-4 : bond 0.00516 ( 7) link_BETA1-4 : angle 2.08756 ( 21) hydrogen bonds : bond 0.05033 ( 580) hydrogen bonds : angle 4.29100 ( 1680) link_BETA1-6 : bond 0.01838 ( 1) link_BETA1-6 : angle 3.16325 ( 3) SS BOND : bond 0.00192 ( 5) SS BOND : angle 0.82259 ( 10) link_BETA1-3 : bond 0.00933 ( 1) link_BETA1-3 : angle 1.19047 ( 3) covalent geometry : bond 0.00458 (11284) covalent geometry : angle 0.70456 (15380) *********************** 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 174 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.8187 (tptt) cc_final: 0.7551 (tptm) REVERT: A 46 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7888 (mmtm) REVERT: A 184 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: A 364 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: A 395 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7387 (mm-30) REVERT: A 396 ASP cc_start: 0.7491 (m-30) cc_final: 0.7247 (m-30) REVERT: A 403 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7457 (tttm) REVERT: A 434 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7606 (tmm160) REVERT: A 666 LYS cc_start: 0.7239 (tptt) cc_final: 0.6561 (ttpp) REVERT: B 270 MET cc_start: 0.7465 (mtp) cc_final: 0.7149 (mtp) REVERT: B 283 PHE cc_start: 0.6690 (m-80) cc_final: 0.6407 (m-80) REVERT: B 383 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8118 (mp) REVERT: C 62 ARG cc_start: 0.6506 (tmm160) cc_final: 0.6167 (tmm160) REVERT: D 33 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8466 (t0) outliers start: 46 outliers final: 15 residues processed: 160 average time/residue: 0.9715 time to fit residues: 172.1900 Evaluate side-chains 127 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 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 605 VAL Chi-restraints excluded: chain B residue 383 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 68 VAL Chi-restraints excluded: chain D residue 77 ILE 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: 0.7980 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 chunk 101 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.152992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117158 restraints weight = 13099.992| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.34 r_work: 0.3242 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11310 Z= 0.112 Angle : 0.599 12.224 15453 Z= 0.286 Chirality : 0.042 0.239 1844 Planarity : 0.004 0.070 1850 Dihedral : 10.160 98.278 2172 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.79 % Allowed : 14.83 % Favored : 82.37 % 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: 0.10 (0.23), residues: 1325 helix: 1.51 (0.20), residues: 719 sheet: -1.12 (0.43), residues: 132 loop : -1.88 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 74 HIS 0.005 0.001 HIS C 197 PHE 0.030 0.001 PHE A 302 TYR 0.016 0.001 TYR A 569 ARG 0.004 0.000 ARG A 539 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 12) link_NAG-ASN : angle 2.50755 ( 36) link_BETA1-4 : bond 0.00529 ( 7) link_BETA1-4 : angle 1.83448 ( 21) hydrogen bonds : bond 0.03910 ( 580) hydrogen bonds : angle 4.10056 ( 1680) link_BETA1-6 : bond 0.01698 ( 1) link_BETA1-6 : angle 3.40981 ( 3) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.70073 ( 10) link_BETA1-3 : bond 0.00726 ( 1) link_BETA1-3 : angle 1.85030 ( 3) covalent geometry : bond 0.00240 (11284) covalent geometry : angle 0.58103 (15380) *********************** 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 151 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: E 53 LYS cc_start: 0.8178 (tptt) cc_final: 0.7437 (tptm) REVERT: A 46 LYS cc_start: 0.8258 (mmmm) cc_final: 0.7803 (mmtm) REVERT: A 150 ASN cc_start: 0.8274 (p0) cc_final: 0.7813 (m-40) REVERT: A 395 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7394 (mm-30) REVERT: A 403 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7636 (tttm) REVERT: A 434 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7549 (tmm160) REVERT: A 582 THR cc_start: 0.7055 (OUTLIER) cc_final: 0.6700 (p) REVERT: A 619 ARG cc_start: 0.5417 (OUTLIER) cc_final: 0.5135 (ptt-90) REVERT: B 270 MET cc_start: 0.7290 (mtp) cc_final: 0.6923 (mtp) REVERT: C 62 ARG cc_start: 0.6574 (tmm160) cc_final: 0.6248 (tmm160) REVERT: C 117 MET cc_start: 0.8583 (mtp) cc_final: 0.8244 (mtt) outliers start: 32 outliers final: 15 residues processed: 143 average time/residue: 0.9152 time to fit residues: 145.1379 Evaluate side-chains 123 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 115 THR 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 400 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain B residue 248 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 130 optimal weight: 0.4980 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN ** 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 = 0.3736 r_free = 0.3736 target = 0.149890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114198 restraints weight = 13168.762| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.34 r_work: 0.3166 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11310 Z= 0.146 Angle : 0.632 12.550 15453 Z= 0.300 Chirality : 0.043 0.245 1844 Planarity : 0.004 0.059 1850 Dihedral : 9.661 77.147 2172 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.93 % Allowed : 15.45 % Favored : 80.63 % 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: 718 sheet: -0.97 (0.43), residues: 132 loop : -1.78 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 74 HIS 0.007 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.016 0.001 TYR A 337 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 12) link_NAG-ASN : angle 2.73963 ( 36) link_BETA1-4 : bond 0.00567 ( 7) link_BETA1-4 : angle 1.70586 ( 21) hydrogen bonds : bond 0.04179 ( 580) hydrogen bonds : angle 4.03239 ( 1680) link_BETA1-6 : bond 0.01414 ( 1) link_BETA1-6 : angle 3.39807 ( 3) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.71514 ( 10) link_BETA1-3 : bond 0.00790 ( 1) link_BETA1-3 : angle 1.77037 ( 3) covalent geometry : bond 0.00346 (11284) covalent geometry : angle 0.61410 (15380) *********************** 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 155 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8280 (mp) REVERT: A 46 LYS cc_start: 0.8273 (mmmm) cc_final: 0.7794 (mmtm) REVERT: A 150 ASN cc_start: 0.8282 (p0) cc_final: 0.7905 (m-40) REVERT: A 184 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: A 364 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: A 395 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 403 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7657 (tttm) REVERT: A 582 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7065 (p) REVERT: B 270 MET cc_start: 0.7249 (mtp) cc_final: 0.6908 (mtp) REVERT: B 383 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8048 (mp) REVERT: B 435 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7640 (mp) REVERT: D 91 TYR cc_start: 0.8425 (m-80) cc_final: 0.8215 (m-80) outliers start: 45 outliers final: 19 residues processed: 142 average time/residue: 1.0321 time to fit residues: 161.8828 Evaluate side-chains 130 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR 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: 0.9990 chunk 57 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.157556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122149 restraints weight = 13214.391| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.28 r_work: 0.3350 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11310 Z= 0.171 Angle : 0.656 12.518 15453 Z= 0.311 Chirality : 0.044 0.242 1844 Planarity : 0.004 0.051 1850 Dihedral : 9.384 75.557 2172 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.75 % Allowed : 15.53 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.24), residues: 1325 helix: 1.61 (0.20), residues: 726 sheet: -0.67 (0.45), residues: 126 loop : -1.74 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 74 HIS 0.008 0.001 HIS C 197 PHE 0.033 0.002 PHE A 302 TYR 0.016 0.002 TYR C 218 ARG 0.007 0.000 ARG C 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 12) link_NAG-ASN : angle 2.71828 ( 36) link_BETA1-4 : bond 0.00428 ( 7) link_BETA1-4 : angle 1.82756 ( 21) hydrogen bonds : bond 0.04379 ( 580) hydrogen bonds : angle 4.06215 ( 1680) link_BETA1-6 : bond 0.01008 ( 1) link_BETA1-6 : angle 3.67644 ( 3) SS BOND : bond 0.00278 ( 5) SS BOND : angle 0.73116 ( 10) link_BETA1-3 : bond 0.00779 ( 1) link_BETA1-3 : angle 1.58230 ( 3) covalent geometry : bond 0.00414 (11284) covalent geometry : angle 0.63777 (15380) *********************** 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 154 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 46 LYS cc_start: 0.8270 (mmmm) cc_final: 0.7898 (mmtm) REVERT: A 118 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8337 (mp) REVERT: A 150 ASN cc_start: 0.8284 (p0) cc_final: 0.7984 (m-40) REVERT: A 184 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: A 364 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: A 365 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 395 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7393 (tp30) REVERT: A 403 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7651 (tttm) REVERT: A 582 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7349 (p) REVERT: B 270 MET cc_start: 0.7308 (mtp) cc_final: 0.6977 (mtp) REVERT: B 383 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 430 LYS cc_start: 0.7660 (mtpt) cc_final: 0.7367 (mtmm) REVERT: C 146 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8171 (m) REVERT: D 91 TYR cc_start: 0.8459 (m-80) cc_final: 0.8225 (m-80) outliers start: 43 outliers final: 22 residues processed: 142 average time/residue: 0.9687 time to fit residues: 151.8306 Evaluate side-chains 133 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 118 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 59 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 50 optimal weight: 0.0070 chunk 101 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.161798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128107 restraints weight = 13115.563| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.20 r_work: 0.3409 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11310 Z= 0.101 Angle : 0.571 12.060 15453 Z= 0.270 Chirality : 0.041 0.253 1844 Planarity : 0.004 0.042 1850 Dihedral : 8.893 75.646 2172 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 2.44 % Allowed : 17.10 % Favored : 80.45 % 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: 0.68 (0.24), residues: 1325 helix: 1.91 (0.20), residues: 726 sheet: -0.70 (0.45), residues: 130 loop : -1.61 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 74 HIS 0.004 0.001 HIS A 553 PHE 0.028 0.001 PHE A 302 TYR 0.015 0.001 TYR A 569 ARG 0.002 0.000 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 12) link_NAG-ASN : angle 2.18197 ( 36) link_BETA1-4 : bond 0.00390 ( 7) link_BETA1-4 : angle 1.42061 ( 21) hydrogen bonds : bond 0.03404 ( 580) hydrogen bonds : angle 3.91560 ( 1680) link_BETA1-6 : bond 0.00945 ( 1) link_BETA1-6 : angle 3.32580 ( 3) SS BOND : bond 0.00129 ( 5) SS BOND : angle 0.52882 ( 10) link_BETA1-3 : bond 0.00779 ( 1) link_BETA1-3 : angle 1.35269 ( 3) covalent geometry : bond 0.00212 (11284) covalent geometry : angle 0.55732 (15380) *********************** 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: 28 poor density : 110 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: E 51 MET cc_start: 0.8800 (ttm) cc_final: 0.8311 (ttp) REVERT: A 46 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7983 (mmtm) REVERT: A 150 ASN cc_start: 0.8286 (p0) cc_final: 0.8067 (m-40) REVERT: A 184 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: A 283 ASP cc_start: 0.8979 (p0) cc_final: 0.8705 (p0) REVERT: A 395 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7468 (tp30) REVERT: A 403 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7718 (tttm) REVERT: A 582 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7434 (p) REVERT: B 145 VAL cc_start: 0.7900 (p) cc_final: 0.7459 (m) REVERT: B 270 MET cc_start: 0.7374 (mtp) cc_final: 0.7104 (mtp) REVERT: B 435 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7556 (mp) REVERT: C 117 MET cc_start: 0.8618 (mtp) cc_final: 0.8308 (mtt) REVERT: D 91 TYR cc_start: 0.8553 (m-80) cc_final: 0.8312 (m-80) outliers start: 28 outliers final: 13 residues processed: 131 average time/residue: 1.4768 time to fit residues: 213.8354 Evaluate side-chains 120 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 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 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.160210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.125904 restraints weight = 13060.380| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.25 r_work: 0.3396 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11310 Z= 0.111 Angle : 0.615 20.336 15453 Z= 0.285 Chirality : 0.046 0.875 1844 Planarity : 0.004 0.042 1850 Dihedral : 8.702 75.158 2172 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 2.79 % Allowed : 17.28 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.77 (0.24), residues: 1325 helix: 1.97 (0.20), residues: 726 sheet: -0.51 (0.45), residues: 126 loop : -1.59 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 209 HIS 0.005 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.002 0.000 ARG A 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00981 ( 12) link_NAG-ASN : angle 4.61565 ( 36) link_BETA1-4 : bond 0.00370 ( 7) link_BETA1-4 : angle 1.43094 ( 21) hydrogen bonds : bond 0.03526 ( 580) hydrogen bonds : angle 3.91476 ( 1680) link_BETA1-6 : bond 0.00972 ( 1) link_BETA1-6 : angle 3.18809 ( 3) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.56628 ( 10) link_BETA1-3 : bond 0.00806 ( 1) link_BETA1-3 : angle 1.37908 ( 3) covalent geometry : bond 0.00245 (11284) covalent geometry : angle 0.56982 (15380) *********************** 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 141 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7883 (mmtm) REVERT: A 150 ASN cc_start: 0.8260 (p0) cc_final: 0.8057 (m-40) REVERT: A 184 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: A 395 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7407 (tp30) REVERT: A 403 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7777 (ttpp) REVERT: A 582 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7338 (p) REVERT: B 145 VAL cc_start: 0.7795 (p) cc_final: 0.7347 (m) REVERT: B 270 MET cc_start: 0.7195 (mtp) cc_final: 0.6859 (mtp) REVERT: B 435 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7509 (mp) REVERT: D 91 TYR cc_start: 0.8491 (m-80) cc_final: 0.8251 (m-80) outliers start: 32 outliers final: 18 residues processed: 132 average time/residue: 0.9292 time to fit residues: 136.2715 Evaluate side-chains 126 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 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 403 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 248 LEU 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 137 ILE Chi-restraints excluded: chain C residue 192 LEU 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: 0.9980 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.158758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123630 restraints weight = 13342.999| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.29 r_work: 0.3366 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11310 Z= 0.147 Angle : 0.651 20.995 15453 Z= 0.302 Chirality : 0.044 0.464 1844 Planarity : 0.004 0.044 1850 Dihedral : 8.637 74.885 2172 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.09 % Favored : 96.83 % Rotamer: Outliers : 2.44 % Allowed : 17.98 % 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: 0.68 (0.24), residues: 1325 helix: 1.87 (0.20), residues: 727 sheet: -0.45 (0.46), residues: 124 loop : -1.61 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 653 HIS 0.006 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.016 0.001 TYR A 569 ARG 0.002 0.000 ARG A 652 Details of bonding type rmsd link_NAG-ASN : bond 0.01128 ( 12) link_NAG-ASN : angle 5.04895 ( 36) link_BETA1-4 : bond 0.00402 ( 7) link_BETA1-4 : angle 1.61325 ( 21) hydrogen bonds : bond 0.03930 ( 580) hydrogen bonds : angle 3.94851 ( 1680) link_BETA1-6 : bond 0.00941 ( 1) link_BETA1-6 : angle 3.02058 ( 3) SS BOND : bond 0.00221 ( 5) SS BOND : angle 0.64759 ( 10) link_BETA1-3 : bond 0.00822 ( 1) link_BETA1-3 : angle 1.45632 ( 3) covalent geometry : bond 0.00349 (11284) covalent geometry : angle 0.59989 (15380) *********************** 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 132 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7903 (mmtm) REVERT: A 184 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: A 395 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7489 (tp30) REVERT: A 403 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7827 (ttpp) REVERT: A 582 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7485 (p) REVERT: B 145 VAL cc_start: 0.7839 (p) cc_final: 0.7393 (m) REVERT: B 270 MET cc_start: 0.7278 (mtp) cc_final: 0.6922 (mtp) REVERT: C 146 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8167 (m) REVERT: D 91 TYR cc_start: 0.8507 (m-80) cc_final: 0.8274 (m-80) outliers start: 28 outliers final: 15 residues processed: 126 average time/residue: 1.0039 time to fit residues: 139.7273 Evaluate side-chains 123 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 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 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 416 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain 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: 0.0980 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.158650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124195 restraints weight = 13084.109| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.24 r_work: 0.3384 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11310 Z= 0.129 Angle : 0.637 20.375 15453 Z= 0.296 Chirality : 0.044 0.483 1844 Planarity : 0.004 0.042 1850 Dihedral : 8.398 74.711 2172 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 2.18 % Allowed : 18.24 % 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: 0.68 (0.24), residues: 1325 helix: 1.88 (0.20), residues: 727 sheet: -0.51 (0.46), residues: 126 loop : -1.62 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 36 HIS 0.005 0.001 HIS C 197 PHE 0.030 0.001 PHE A 302 TYR 0.016 0.001 TYR A 569 ARG 0.010 0.000 ARG A 543 Details of bonding type rmsd link_NAG-ASN : bond 0.01026 ( 12) link_NAG-ASN : angle 4.78272 ( 36) link_BETA1-4 : bond 0.00338 ( 7) link_BETA1-4 : angle 1.53399 ( 21) hydrogen bonds : bond 0.03777 ( 580) hydrogen bonds : angle 3.96271 ( 1680) link_BETA1-6 : bond 0.00918 ( 1) link_BETA1-6 : angle 2.57580 ( 3) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.58503 ( 10) link_BETA1-3 : bond 0.00827 ( 1) link_BETA1-3 : angle 1.46351 ( 3) covalent geometry : bond 0.00298 (11284) covalent geometry : angle 0.59075 (15380) ********************** 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 127 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: E 51 MET cc_start: 0.8748 (ttm) cc_final: 0.8292 (ttp) REVERT: A 46 LYS cc_start: 0.8262 (mmmm) cc_final: 0.7885 (mmtm) REVERT: A 184 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: A 395 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7436 (tp30) REVERT: A 403 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7818 (ttpp) REVERT: A 582 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7430 (p) REVERT: B 145 VAL cc_start: 0.7821 (p) cc_final: 0.7396 (m) REVERT: B 210 MET cc_start: 0.8525 (mmt) cc_final: 0.8210 (mmm) REVERT: B 270 MET cc_start: 0.7226 (mtp) cc_final: 0.6859 (mtp) REVERT: C 117 MET cc_start: 0.8569 (mtp) cc_final: 0.8247 (mtt) REVERT: C 146 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8125 (m) REVERT: C 167 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7916 (mp) REVERT: D 91 TYR cc_start: 0.8509 (m-80) cc_final: 0.8277 (m-80) outliers start: 25 outliers final: 17 residues processed: 122 average time/residue: 1.0234 time to fit residues: 137.5284 Evaluate side-chains 121 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 121 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 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 416 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119315 restraints weight = 13067.530| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.20 r_work: 0.3349 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11310 Z= 0.172 Angle : 0.681 20.743 15453 Z= 0.318 Chirality : 0.045 0.474 1844 Planarity : 0.004 0.048 1850 Dihedral : 8.415 74.395 2172 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.32 % Favored : 96.60 % Rotamer: Outliers : 2.53 % Allowed : 17.98 % 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: 0.53 (0.24), residues: 1325 helix: 1.74 (0.20), residues: 727 sheet: -0.53 (0.46), residues: 126 loop : -1.66 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 227 HIS 0.008 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.017 0.002 TYR A 337 ARG 0.008 0.000 ARG A 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00986 ( 12) link_NAG-ASN : angle 4.92100 ( 36) link_BETA1-4 : bond 0.00335 ( 7) link_BETA1-4 : angle 1.65274 ( 21) hydrogen bonds : bond 0.04311 ( 580) hydrogen bonds : angle 4.03656 ( 1680) link_BETA1-6 : bond 0.00912 ( 1) link_BETA1-6 : angle 2.34161 ( 3) SS BOND : bond 0.00242 ( 5) SS BOND : angle 0.74863 ( 10) link_BETA1-3 : bond 0.00908 ( 1) link_BETA1-3 : angle 1.69762 ( 3) covalent geometry : bond 0.00418 (11284) covalent geometry : angle 0.63562 (15380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7829.45 seconds wall clock time: 137 minutes 17.71 seconds (8237.71 seconds total)