Starting phenix.real_space_refine on Tue Jul 29 18:11:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c9i_30312/07_2025/7c9i_30312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9i_30312/07_2025/7c9i_30312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c9i_30312/07_2025/7c9i_30312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9i_30312/07_2025/7c9i_30312.map" model { file = "/net/cci-nas-00/data/ceres_data/7c9i_30312/07_2025/7c9i_30312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9i_30312/07_2025/7c9i_30312.cif" } resolution = 3.1 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 C 7123 2.51 5 N 1709 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10853 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5235 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 37, 'TRANS': 629} Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2436 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "E" 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: "F" 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: "G" 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: "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: "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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'FTO': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 125 Unusual residues: {'CLR': 3, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 6.71, per 1000 atoms: 0.62 Number of scatterers: 10853 At special positions: 0 Unit cell: (110.191, 93.826, 133.102, 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 40 16.00 P 2 15.00 O 1979 8.00 N 1709 7.00 C 7123 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.04 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 F 3 " - " BMA F 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " BMA F 3 " - " BMA F 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 E 1 " - " ASN A 45 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN A 435 " " NAG H 1 " - " ASN A 573 " " NAG I 1 " - " ASN A 530 " " NAG J 1 " - " ASN A 562 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2470 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 57.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.578A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 removed outlier: 4.064A pdb=" N TRP A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.732A pdb=" N MET A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.904A pdb=" N ALA A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.715A pdb=" N GLU A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.120A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 240 removed outlier: 3.511A pdb=" N SER A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 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 407 removed outlier: 4.096A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 481 through 503 removed outlier: 3.797A pdb=" N ASP A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 3.780A pdb=" N VAL A 518 " --> pdb=" O ASP A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.701A pdb=" N ARG A 543 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 545 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.530A pdb=" N TYR A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 removed outlier: 3.671A pdb=" N ASP A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.731A pdb=" N GLU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 693 removed outlier: 3.554A pdb=" N LYS A 693 " --> pdb=" O CYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.505A pdb=" N PHE A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 103 removed outlier: 3.581A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (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 159 through 176 removed outlier: 3.924A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 240 removed outlier: 3.500A pdb=" N GLN B 222 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 263 removed outlier: 3.770A pdb=" N SER B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.965A pdb=" N MET B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.640A pdb=" N THR B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 429 removed outlier: 3.746A pdb=" N THR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 408 " --> pdb=" O TRP B 404 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.424A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 removed outlier: 4.229A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.612A pdb=" N PHE C 11 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 Processing helix chain 'C' and resid 30 through 61 removed outlier: 3.511A pdb=" N ILE C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP C 53 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 103 removed outlier: 3.597A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 139 removed outlier: 3.704A pdb=" N MET C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 184 removed outlier: 3.767A pdb=" N VAL C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 203 removed outlier: 4.111A 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 214 through 232 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'D' and resid 7 through 21 removed outlier: 3.550A pdb=" N GLY D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.820A pdb=" N TRP D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 Processing helix chain 'D' and resid 49 through 82 removed outlier: 4.029A pdb=" N GLY D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL D 62 " --> pdb=" O TRP D 58 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU D 71 " --> pdb=" O TRP D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.596A pdb=" N ALA A 658 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 99 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR A 94 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 98 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N PHE A 181 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 121 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU A 183 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 123 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.636A pdb=" N MET A 378 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP A 360 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N VAL A 439 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 362 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 441 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU A 364 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL A 275 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE A 362 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 277 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU A 364 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 279 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 276 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL A 328 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 278 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 330 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR A 280 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 579 removed outlier: 4.262A pdb=" N CYS A 620 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 603 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.603A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 545 hydrogen bonds defined for protein. 1587 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: 2.90 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1639 1.31 - 1.44: 3156 1.44 - 1.56: 6269 1.56 - 1.69: 8 1.69 - 1.81: 61 Bond restraints: 11133 Sorted by residual: bond pdb=" C16 FTO B 502 " pdb=" N17 FTO B 502 " ideal model delta sigma weight residual 1.337 1.451 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C13 FTO B 502 " pdb=" N14 FTO B 502 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C10 FTO B 502 " pdb=" N11 FTO B 502 " ideal model delta sigma weight residual 1.347 1.452 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C04 FTO B 502 " pdb=" N05 FTO B 502 " ideal model delta sigma weight residual 1.350 1.452 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C04 FTO B 502 " pdb=" O03 FTO B 502 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 11128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 14863 3.10 - 6.19: 279 6.19 - 9.29: 33 9.29 - 12.38: 9 12.38 - 15.48: 1 Bond angle restraints: 15185 Sorted by residual: angle pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta sigma weight residual 121.97 131.19 -9.22 1.80e+00 3.09e-01 2.62e+01 angle pdb=" C PHE B 86 " pdb=" N VAL B 87 " pdb=" CA VAL B 87 " ideal model delta sigma weight residual 120.33 124.40 -4.07 8.00e-01 1.56e+00 2.59e+01 angle pdb=" CA LEU B 286 " pdb=" CB LEU B 286 " pdb=" CG LEU B 286 " ideal model delta sigma weight residual 116.30 131.78 -15.48 3.50e+00 8.16e-02 1.96e+01 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 115.79 -5.09 1.22e+00 6.72e-01 1.74e+01 angle pdb=" N ALA A 157 " pdb=" CA ALA A 157 " pdb=" C ALA A 157 " ideal model delta sigma weight residual 110.97 115.28 -4.31 1.09e+00 8.42e-01 1.56e+01 ... (remaining 15180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.70: 6625 22.70 - 45.40: 197 45.40 - 68.10: 49 68.10 - 90.80: 24 90.80 - 113.51: 18 Dihedral angle restraints: 6913 sinusoidal: 3080 harmonic: 3833 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 -167.45 81.45 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual -180.00 -142.30 -37.70 0 5.00e+00 4.00e-02 5.68e+01 dihedral pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 145.95 -52.95 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1628 0.096 - 0.191: 168 0.191 - 0.287: 12 0.287 - 0.383: 4 0.383 - 0.478: 1 Chirality restraints: 1813 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 573 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C2 NAG I 2 " pdb=" C1 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" N2 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C2 NAG A 804 " pdb=" C1 NAG A 804 " pdb=" C3 NAG A 804 " pdb=" N2 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.49 -2.13 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 1810 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 227 " -0.027 2.00e-02 2.50e+03 2.11e-02 1.12e+01 pdb=" CG TRP C 227 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 227 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 227 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 227 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 227 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 227 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 227 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 227 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 36 " -0.024 2.00e-02 2.50e+03 1.83e-02 8.37e+00 pdb=" CG TRP D 36 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 36 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 36 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 36 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 36 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 36 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO A 560 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " -0.041 5.00e-02 4.00e+02 ... (remaining 1842 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1900 2.77 - 3.30: 9669 3.30 - 3.83: 17429 3.83 - 4.37: 20748 4.37 - 4.90: 36534 Nonbonded interactions: 86280 Sorted by model distance: nonbonded pdb=" OD1 ASP A 253 " pdb=" OG1 THR A 561 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 632 " pdb=" O TYR A 645 " model vdw 2.240 3.040 nonbonded pdb=" O PHE B 445 " pdb=" OG1 THR B 449 " model vdw 2.282 3.040 nonbonded pdb=" OG SER D 7 " pdb=" OE1 GLU D 9 " model vdw 2.293 3.040 nonbonded pdb=" O GLU D 40 " pdb=" OH TYR D 47 " model vdw 2.303 3.040 ... (remaining 86275 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 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 3.010 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.008 0.114 11158 Z= 0.353 Angle : 1.096 15.481 15256 Z= 0.551 Chirality : 0.062 0.478 1813 Planarity : 0.008 0.071 1833 Dihedral : 14.169 113.506 4431 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.18 % Allowed : 2.04 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.93 (0.18), residues: 1303 helix: -2.14 (0.15), residues: 702 sheet: -1.99 (0.40), residues: 125 loop : -3.33 (0.22), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 227 HIS 0.026 0.003 HIS C 197 PHE 0.038 0.004 PHE C 132 TYR 0.038 0.003 TYR A 565 ARG 0.010 0.001 ARG A 429 Details of bonding type rmsd link_NAG-ASN : bond 0.01070 ( 12) link_NAG-ASN : angle 5.05670 ( 36) link_BETA1-4 : bond 0.00603 ( 7) link_BETA1-4 : angle 2.60600 ( 21) hydrogen bonds : bond 0.18515 ( 545) hydrogen bonds : angle 6.91153 ( 1587) link_BETA1-6 : bond 0.00405 ( 1) link_BETA1-6 : angle 1.49457 ( 3) SS BOND : bond 0.00526 ( 4) SS BOND : angle 2.15415 ( 8) link_BETA1-3 : bond 0.00062 ( 1) link_BETA1-3 : angle 1.42955 ( 3) covalent geometry : bond 0.00788 (11133) covalent geometry : angle 1.06473 (15185) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 1.107 Fit side-chains REVERT: A 246 ILE cc_start: 0.8339 (mm) cc_final: 0.8096 (mt) REVERT: A 693 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8549 (mmtp) REVERT: B 165 TRP cc_start: 0.7283 (t60) cc_final: 0.6738 (t60) REVERT: B 169 SER cc_start: 0.9116 (t) cc_final: 0.8475 (p) REVERT: C 237 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6781 (mtt-85) REVERT: D 54 LYS cc_start: 0.7488 (ttpt) cc_final: 0.6874 (ttpp) REVERT: D 91 TYR cc_start: 0.7591 (m-80) cc_final: 0.6970 (m-80) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 0.2743 time to fit residues: 73.5097 Evaluate side-chains 132 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 380 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 163 GLN A 222 HIS A 355 GLN A 385 GLN A 454 GLN A 531 ASN A 606 GLN B 454 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113380 restraints weight = 13460.404| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.81 r_work: 0.2987 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11158 Z= 0.148 Angle : 0.690 11.918 15256 Z= 0.333 Chirality : 0.045 0.255 1813 Planarity : 0.005 0.048 1833 Dihedral : 12.909 115.991 2127 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.60 % Allowed : 6.13 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.79 (0.21), residues: 1303 helix: -0.08 (0.19), residues: 707 sheet: -1.78 (0.40), residues: 120 loop : -2.69 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 209 HIS 0.009 0.001 HIS C 197 PHE 0.033 0.002 PHE A 302 TYR 0.014 0.002 TYR A 337 ARG 0.005 0.001 ARG A 391 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 12) link_NAG-ASN : angle 3.28247 ( 36) link_BETA1-4 : bond 0.00464 ( 7) link_BETA1-4 : angle 1.77859 ( 21) hydrogen bonds : bond 0.05217 ( 545) hydrogen bonds : angle 4.45296 ( 1587) link_BETA1-6 : bond 0.01204 ( 1) link_BETA1-6 : angle 2.01653 ( 3) SS BOND : bond 0.00754 ( 4) SS BOND : angle 1.10445 ( 8) link_BETA1-3 : bond 0.00898 ( 1) link_BETA1-3 : angle 1.91044 ( 3) covalent geometry : bond 0.00337 (11133) covalent geometry : angle 0.66823 (15185) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.176 Fit side-chains REVERT: A 99 GLU cc_start: 0.8330 (tp30) cc_final: 0.8130 (tt0) REVERT: A 237 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7521 (mm-40) REVERT: A 246 ILE cc_start: 0.8522 (mm) cc_final: 0.8283 (mt) REVERT: A 343 MET cc_start: 0.9071 (tpp) cc_final: 0.8676 (tpp) REVERT: A 474 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 636 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7680 (mm-30) REVERT: A 693 LYS cc_start: 0.8815 (mmtp) cc_final: 0.8578 (mmtp) REVERT: B 80 LYS cc_start: 0.8566 (tttt) cc_final: 0.8049 (tppt) REVERT: B 165 TRP cc_start: 0.7640 (t60) cc_final: 0.7061 (t60) REVERT: B 169 SER cc_start: 0.9175 (t) cc_final: 0.8669 (p) REVERT: B 210 MET cc_start: 0.9052 (mmt) cc_final: 0.8394 (mmt) REVERT: B 280 GLU cc_start: 0.6463 (pt0) cc_final: 0.6197 (pt0) REVERT: C 140 ASP cc_start: 0.8525 (m-30) cc_final: 0.8304 (m-30) REVERT: C 237 ARG cc_start: 0.7036 (mtt180) cc_final: 0.6740 (mtt-85) REVERT: D 34 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8192 (mp) REVERT: D 54 LYS cc_start: 0.7377 (ttpt) cc_final: 0.7024 (ttpp) REVERT: D 91 TYR cc_start: 0.7964 (m-80) cc_final: 0.7548 (m-80) outliers start: 18 outliers final: 11 residues processed: 152 average time/residue: 0.3252 time to fit residues: 70.8275 Evaluate side-chains 133 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS D 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112974 restraints weight = 13660.732| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.84 r_work: 0.3093 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11158 Z= 0.149 Angle : 0.649 13.254 15256 Z= 0.310 Chirality : 0.044 0.241 1813 Planarity : 0.004 0.057 1833 Dihedral : 10.931 115.751 2123 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.49 % Allowed : 8.26 % Favored : 89.25 % 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: -0.87 (0.23), residues: 1303 helix: 0.79 (0.20), residues: 708 sheet: -1.63 (0.40), residues: 126 loop : -2.44 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 209 HIS 0.006 0.001 HIS C 197 PHE 0.033 0.002 PHE A 302 TYR 0.015 0.002 TYR A 569 ARG 0.002 0.000 ARG A 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 12) link_NAG-ASN : angle 2.82096 ( 36) link_BETA1-4 : bond 0.00337 ( 7) link_BETA1-4 : angle 1.72939 ( 21) hydrogen bonds : bond 0.04659 ( 545) hydrogen bonds : angle 4.11094 ( 1587) link_BETA1-6 : bond 0.01310 ( 1) link_BETA1-6 : angle 2.21238 ( 3) SS BOND : bond 0.00308 ( 4) SS BOND : angle 0.85007 ( 8) link_BETA1-3 : bond 0.00972 ( 1) link_BETA1-3 : angle 1.48868 ( 3) covalent geometry : bond 0.00353 (11133) covalent geometry : angle 0.63095 (15185) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.092 Fit side-chains REVERT: A 99 GLU cc_start: 0.8296 (tp30) cc_final: 0.8072 (tt0) REVERT: A 253 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8327 (t70) REVERT: A 343 MET cc_start: 0.9046 (tpp) cc_final: 0.8683 (tpp) REVERT: A 474 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 636 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 693 LYS cc_start: 0.8856 (mmtp) cc_final: 0.8613 (mmtp) REVERT: A 699 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7476 (pp) REVERT: B 80 LYS cc_start: 0.8608 (tttt) cc_final: 0.8141 (tppt) REVERT: B 159 TYR cc_start: 0.6307 (m-80) cc_final: 0.5955 (m-80) REVERT: B 169 SER cc_start: 0.9165 (t) cc_final: 0.8649 (p) REVERT: B 210 MET cc_start: 0.8932 (mmt) cc_final: 0.8351 (mmt) REVERT: B 258 LEU cc_start: 0.8166 (tp) cc_final: 0.7911 (tp) REVERT: B 280 GLU cc_start: 0.6246 (pt0) cc_final: 0.5926 (pt0) REVERT: C 184 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7770 (mtt180) REVERT: C 237 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6780 (mtt-85) REVERT: D 34 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8209 (mp) REVERT: D 91 TYR cc_start: 0.8038 (m-80) cc_final: 0.7651 (m-80) outliers start: 28 outliers final: 17 residues processed: 134 average time/residue: 0.3243 time to fit residues: 60.6021 Evaluate side-chains 128 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 77 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 109 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 63 GLN A 610 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.101507 restraints weight = 14011.064| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.93 r_work: 0.2936 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11158 Z= 0.150 Angle : 0.638 13.266 15256 Z= 0.305 Chirality : 0.044 0.244 1813 Planarity : 0.004 0.043 1833 Dihedral : 9.820 111.081 2123 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.31 % Allowed : 9.33 % Favored : 88.37 % 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: -0.41 (0.23), residues: 1303 helix: 1.21 (0.20), residues: 709 sheet: -1.45 (0.43), residues: 119 loop : -2.30 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 209 HIS 0.005 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.015 0.001 TYR D 47 ARG 0.004 0.000 ARG A 626 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 12) link_NAG-ASN : angle 2.70124 ( 36) link_BETA1-4 : bond 0.00293 ( 7) link_BETA1-4 : angle 1.83303 ( 21) hydrogen bonds : bond 0.04410 ( 545) hydrogen bonds : angle 3.98778 ( 1587) link_BETA1-6 : bond 0.01467 ( 1) link_BETA1-6 : angle 3.72882 ( 3) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.99112 ( 8) link_BETA1-3 : bond 0.00681 ( 1) link_BETA1-3 : angle 1.59646 ( 3) covalent geometry : bond 0.00364 (11133) covalent geometry : angle 0.61912 (15185) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 2.363 Fit side-chains REVERT: A 99 GLU cc_start: 0.8299 (tp30) cc_final: 0.8047 (tt0) REVERT: A 138 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.8943 (m) REVERT: A 343 MET cc_start: 0.9045 (tpp) cc_final: 0.8661 (tpp) REVERT: A 474 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 693 LYS cc_start: 0.8989 (mmtp) cc_final: 0.8749 (mmtp) REVERT: A 699 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7503 (pp) REVERT: B 80 LYS cc_start: 0.8536 (tttt) cc_final: 0.8064 (tppt) REVERT: B 159 TYR cc_start: 0.6296 (m-80) cc_final: 0.6008 (m-80) REVERT: B 169 SER cc_start: 0.9165 (t) cc_final: 0.8657 (p) REVERT: B 241 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7171 (mp) REVERT: B 280 GLU cc_start: 0.6332 (pt0) cc_final: 0.5994 (pt0) REVERT: C 138 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8278 (mp) REVERT: C 230 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8348 (mm) REVERT: C 237 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6752 (mtt-85) REVERT: D 34 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8190 (mp) REVERT: D 43 LEU cc_start: 0.8088 (mt) cc_final: 0.7823 (mp) REVERT: D 80 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8170 (mp) REVERT: D 91 TYR cc_start: 0.8069 (m-80) cc_final: 0.7679 (m-80) outliers start: 26 outliers final: 16 residues processed: 138 average time/residue: 0.5130 time to fit residues: 100.6743 Evaluate side-chains 135 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 0.0050 chunk 80 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN B 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102363 restraints weight = 13983.898| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.93 r_work: 0.2936 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11158 Z= 0.129 Angle : 0.602 12.736 15256 Z= 0.289 Chirality : 0.043 0.243 1813 Planarity : 0.004 0.040 1833 Dihedral : 9.424 106.287 2123 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.58 % Allowed : 10.66 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1303 helix: 1.45 (0.20), residues: 712 sheet: -1.21 (0.41), residues: 130 loop : -2.24 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 209 HIS 0.004 0.001 HIS C 197 PHE 0.030 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.003 0.000 ARG C 241 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 12) link_NAG-ASN : angle 2.41700 ( 36) link_BETA1-4 : bond 0.00272 ( 7) link_BETA1-4 : angle 1.69073 ( 21) hydrogen bonds : bond 0.04075 ( 545) hydrogen bonds : angle 3.87146 ( 1587) link_BETA1-6 : bond 0.01462 ( 1) link_BETA1-6 : angle 3.14337 ( 3) SS BOND : bond 0.00257 ( 4) SS BOND : angle 0.71571 ( 8) link_BETA1-3 : bond 0.00851 ( 1) link_BETA1-3 : angle 1.61144 ( 3) covalent geometry : bond 0.00305 (11133) covalent geometry : angle 0.58664 (15185) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.264 Fit side-chains REVERT: A 99 GLU cc_start: 0.8269 (tp30) cc_final: 0.8021 (tt0) REVERT: A 138 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8939 (m) REVERT: A 215 MET cc_start: 0.9273 (ttm) cc_final: 0.9036 (ttp) REVERT: A 343 MET cc_start: 0.9040 (tpp) cc_final: 0.8637 (tpp) REVERT: A 693 LYS cc_start: 0.8988 (mmtp) cc_final: 0.8745 (mmtp) REVERT: A 699 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7507 (pp) REVERT: B 80 LYS cc_start: 0.8527 (tttt) cc_final: 0.8056 (tppt) REVERT: B 169 SER cc_start: 0.9118 (t) cc_final: 0.8613 (p) REVERT: B 258 LEU cc_start: 0.8153 (tp) cc_final: 0.7926 (tp) REVERT: B 280 GLU cc_start: 0.6218 (pt0) cc_final: 0.5891 (pt0) REVERT: C 138 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8247 (mp) REVERT: C 230 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8326 (mm) REVERT: C 237 ARG cc_start: 0.7022 (mtt180) cc_final: 0.6763 (mtt-85) REVERT: D 80 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8206 (mp) REVERT: D 91 TYR cc_start: 0.7959 (m-80) cc_final: 0.7639 (m-80) outliers start: 29 outliers final: 15 residues processed: 141 average time/residue: 0.2424 time to fit residues: 48.6870 Evaluate side-chains 136 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 125 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 101 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103881 restraints weight = 14015.847| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.93 r_work: 0.2956 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11158 Z= 0.115 Angle : 0.589 12.504 15256 Z= 0.280 Chirality : 0.042 0.245 1813 Planarity : 0.004 0.041 1833 Dihedral : 9.024 93.473 2123 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.49 % Allowed : 11.28 % Favored : 86.23 % 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: 0.12 (0.24), residues: 1303 helix: 1.64 (0.20), residues: 713 sheet: -1.09 (0.42), residues: 130 loop : -2.14 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 209 HIS 0.003 0.001 HIS A 553 PHE 0.029 0.001 PHE A 302 TYR 0.013 0.001 TYR A 569 ARG 0.003 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 12) link_NAG-ASN : angle 2.32647 ( 36) link_BETA1-4 : bond 0.00295 ( 7) link_BETA1-4 : angle 1.54628 ( 21) hydrogen bonds : bond 0.03825 ( 545) hydrogen bonds : angle 3.77807 ( 1587) link_BETA1-6 : bond 0.01604 ( 1) link_BETA1-6 : angle 3.54426 ( 3) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.62321 ( 8) link_BETA1-3 : bond 0.00687 ( 1) link_BETA1-3 : angle 1.50209 ( 3) covalent geometry : bond 0.00266 (11133) covalent geometry : angle 0.57431 (15185) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.103 Fit side-chains REVERT: A 99 GLU cc_start: 0.8257 (tp30) cc_final: 0.8013 (tt0) REVERT: A 138 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8941 (m) REVERT: A 215 MET cc_start: 0.9267 (ttm) cc_final: 0.9042 (ttp) REVERT: A 693 LYS cc_start: 0.9010 (mmtp) cc_final: 0.8764 (mmtp) REVERT: A 699 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7533 (pp) REVERT: B 80 LYS cc_start: 0.8476 (tttt) cc_final: 0.8013 (tppt) REVERT: B 169 SER cc_start: 0.9111 (t) cc_final: 0.8608 (p) REVERT: B 258 LEU cc_start: 0.8139 (tp) cc_final: 0.7892 (tp) REVERT: C 184 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7651 (mtt180) REVERT: C 230 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8322 (mm) REVERT: C 237 ARG cc_start: 0.6986 (mtt180) cc_final: 0.6757 (mtt-85) REVERT: D 59 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7260 (mtp180) REVERT: D 80 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8216 (mp) REVERT: D 91 TYR cc_start: 0.8043 (m-80) cc_final: 0.7733 (m-80) outliers start: 28 outliers final: 16 residues processed: 138 average time/residue: 0.2407 time to fit residues: 46.9819 Evaluate side-chains 135 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 44 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.099256 restraints weight = 14240.705| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.94 r_work: 0.2899 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11158 Z= 0.195 Angle : 0.668 13.959 15256 Z= 0.318 Chirality : 0.046 0.244 1813 Planarity : 0.004 0.041 1833 Dihedral : 9.005 79.148 2123 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.58 % Allowed : 11.90 % Favored : 85.52 % 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: -0.00 (0.24), residues: 1303 helix: 1.51 (0.20), residues: 712 sheet: -1.15 (0.42), residues: 130 loop : -2.15 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 257 HIS 0.005 0.001 HIS C 197 PHE 0.031 0.002 PHE A 302 TYR 0.016 0.002 TYR A 569 ARG 0.003 0.001 ARG A 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 12) link_NAG-ASN : angle 2.62871 ( 36) link_BETA1-4 : bond 0.00201 ( 7) link_BETA1-4 : angle 1.80132 ( 21) hydrogen bonds : bond 0.04675 ( 545) hydrogen bonds : angle 3.91590 ( 1587) link_BETA1-6 : bond 0.01328 ( 1) link_BETA1-6 : angle 3.21143 ( 3) SS BOND : bond 0.00281 ( 4) SS BOND : angle 0.86603 ( 8) link_BETA1-3 : bond 0.00510 ( 1) link_BETA1-3 : angle 1.91389 ( 3) covalent geometry : bond 0.00479 (11133) covalent geometry : angle 0.65092 (15185) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.073 Fit side-chains REVERT: A 99 GLU cc_start: 0.8286 (tp30) cc_final: 0.8058 (tt0) REVERT: A 138 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.8973 (m) REVERT: A 343 MET cc_start: 0.9080 (tpp) cc_final: 0.8727 (tpp) REVERT: A 693 LYS cc_start: 0.8997 (mmtp) cc_final: 0.8718 (mmtp) REVERT: A 699 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7445 (pp) REVERT: B 80 LYS cc_start: 0.8576 (tttt) cc_final: 0.8107 (tppt) REVERT: B 163 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.6963 (t-90) REVERT: B 169 SER cc_start: 0.9124 (t) cc_final: 0.8556 (p) REVERT: B 280 GLU cc_start: 0.6067 (pt0) cc_final: 0.5738 (pt0) REVERT: C 184 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7735 (mtt180) REVERT: C 237 ARG cc_start: 0.7027 (mtt180) cc_final: 0.6777 (mtt-85) REVERT: D 80 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8174 (mp) REVERT: D 91 TYR cc_start: 0.7988 (m-80) cc_final: 0.7755 (m-80) outliers start: 29 outliers final: 19 residues processed: 136 average time/residue: 0.2433 time to fit residues: 46.1916 Evaluate side-chains 134 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 80 optimal weight: 0.0370 chunk 120 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.103948 restraints weight = 13935.519| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.91 r_work: 0.2950 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11158 Z= 0.116 Angle : 0.586 12.435 15256 Z= 0.280 Chirality : 0.042 0.240 1813 Planarity : 0.004 0.040 1833 Dihedral : 8.415 76.722 2123 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.66 % Allowed : 11.81 % Favored : 85.52 % 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: 0.30 (0.24), residues: 1303 helix: 1.74 (0.20), residues: 719 sheet: -1.07 (0.42), residues: 130 loop : -2.02 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 209 HIS 0.003 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.013 0.001 TYR A 569 ARG 0.002 0.000 ARG A 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 12) link_NAG-ASN : angle 2.27226 ( 36) link_BETA1-4 : bond 0.00317 ( 7) link_BETA1-4 : angle 1.53201 ( 21) hydrogen bonds : bond 0.03856 ( 545) hydrogen bonds : angle 3.76237 ( 1587) link_BETA1-6 : bond 0.00959 ( 1) link_BETA1-6 : angle 3.12193 ( 3) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.62905 ( 8) link_BETA1-3 : bond 0.00791 ( 1) link_BETA1-3 : angle 1.20982 ( 3) covalent geometry : bond 0.00268 (11133) covalent geometry : angle 0.57184 (15185) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 1.184 Fit side-chains REVERT: A 99 GLU cc_start: 0.8222 (tp30) cc_final: 0.7983 (tt0) REVERT: A 138 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8931 (m) REVERT: A 215 MET cc_start: 0.9288 (ttm) cc_final: 0.9059 (ttp) REVERT: A 693 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8658 (mmtp) REVERT: A 699 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7448 (pp) REVERT: B 80 LYS cc_start: 0.8349 (tttt) cc_final: 0.7868 (tppt) REVERT: B 163 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.6951 (t-90) REVERT: B 169 SER cc_start: 0.9094 (t) cc_final: 0.8576 (p) REVERT: B 258 LEU cc_start: 0.8137 (tp) cc_final: 0.7899 (tp) REVERT: C 230 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8301 (mm) REVERT: D 59 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7287 (mtp180) REVERT: D 80 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8135 (mp) REVERT: D 91 TYR cc_start: 0.7953 (m-80) cc_final: 0.7702 (m-80) outliers start: 30 outliers final: 18 residues processed: 144 average time/residue: 0.2418 time to fit residues: 49.8188 Evaluate side-chains 137 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 PHE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 80 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 104 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 128 optimal weight: 0.0010 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 overall best weight: 1.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.097034 restraints weight = 14197.599| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.96 r_work: 0.2905 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11158 Z= 0.235 Angle : 0.712 14.174 15256 Z= 0.339 Chirality : 0.047 0.246 1813 Planarity : 0.004 0.042 1833 Dihedral : 8.795 78.315 2123 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.58 % Allowed : 11.81 % Favored : 85.61 % 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: -0.03 (0.24), residues: 1303 helix: 1.43 (0.20), residues: 718 sheet: -1.13 (0.42), residues: 130 loop : -2.10 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.005 0.001 HIS C 197 PHE 0.032 0.002 PHE A 302 TYR 0.017 0.002 TYR C 210 ARG 0.010 0.001 ARG A 391 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 12) link_NAG-ASN : angle 2.77690 ( 36) link_BETA1-4 : bond 0.00166 ( 7) link_BETA1-4 : angle 1.89848 ( 21) hydrogen bonds : bond 0.05022 ( 545) hydrogen bonds : angle 3.97795 ( 1587) link_BETA1-6 : bond 0.00986 ( 1) link_BETA1-6 : angle 2.85345 ( 3) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.86801 ( 8) link_BETA1-3 : bond 0.00506 ( 1) link_BETA1-3 : angle 1.95109 ( 3) covalent geometry : bond 0.00582 (11133) covalent geometry : angle 0.69489 (15185) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.094 Fit side-chains REVERT: A 99 GLU cc_start: 0.8270 (tp30) cc_final: 0.8049 (tt0) REVERT: A 138 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.8958 (m) REVERT: A 343 MET cc_start: 0.9083 (tpp) cc_final: 0.8758 (tpp) REVERT: A 693 LYS cc_start: 0.9014 (mmtp) cc_final: 0.8697 (mmtp) REVERT: A 699 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7460 (pp) REVERT: B 80 LYS cc_start: 0.8592 (tttt) cc_final: 0.8101 (tppt) REVERT: B 163 HIS cc_start: 0.7532 (OUTLIER) cc_final: 0.6964 (t-90) REVERT: B 169 SER cc_start: 0.9128 (t) cc_final: 0.8540 (p) REVERT: B 258 LEU cc_start: 0.8221 (tp) cc_final: 0.7977 (tp) REVERT: D 91 TYR cc_start: 0.7906 (m-80) cc_final: 0.7648 (m-80) outliers start: 29 outliers final: 22 residues processed: 135 average time/residue: 0.2552 time to fit residues: 48.5674 Evaluate side-chains 134 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 0.0370 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102663 restraints weight = 13926.912| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.91 r_work: 0.2949 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11158 Z= 0.112 Angle : 0.590 11.777 15256 Z= 0.283 Chirality : 0.043 0.245 1813 Planarity : 0.004 0.039 1833 Dihedral : 8.142 75.011 2123 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.13 % Allowed : 12.52 % Favored : 85.35 % 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: 0.35 (0.24), residues: 1303 helix: 1.74 (0.20), residues: 719 sheet: -1.01 (0.43), residues: 129 loop : -1.94 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 209 HIS 0.003 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.013 0.001 TYR A 569 ARG 0.009 0.000 ARG A 391 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 12) link_NAG-ASN : angle 2.23476 ( 36) link_BETA1-4 : bond 0.00288 ( 7) link_BETA1-4 : angle 1.53045 ( 21) hydrogen bonds : bond 0.03868 ( 545) hydrogen bonds : angle 3.78370 ( 1587) link_BETA1-6 : bond 0.00891 ( 1) link_BETA1-6 : angle 2.74901 ( 3) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.66203 ( 8) link_BETA1-3 : bond 0.00782 ( 1) link_BETA1-3 : angle 1.20808 ( 3) covalent geometry : bond 0.00254 (11133) covalent geometry : angle 0.57718 (15185) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.190 Fit side-chains REVERT: A 99 GLU cc_start: 0.8252 (tp30) cc_final: 0.7987 (tt0) REVERT: A 138 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8936 (m) REVERT: A 215 MET cc_start: 0.9299 (ttm) cc_final: 0.9093 (ttp) REVERT: A 699 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7448 (pp) REVERT: B 80 LYS cc_start: 0.8393 (tttt) cc_final: 0.7917 (tppt) REVERT: B 163 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6903 (t-90) REVERT: B 169 SER cc_start: 0.9110 (t) cc_final: 0.8601 (p) REVERT: C 230 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8322 (mm) REVERT: D 59 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7321 (mtt180) REVERT: D 91 TYR cc_start: 0.7960 (m-80) cc_final: 0.7681 (m-80) outliers start: 24 outliers final: 17 residues processed: 135 average time/residue: 0.2433 time to fit residues: 46.2146 Evaluate side-chains 135 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 59 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 0.0270 chunk 73 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN D 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.128536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.102115 restraints weight = 13844.812| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.90 r_work: 0.2946 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11158 Z= 0.129 Angle : 0.604 12.240 15256 Z= 0.289 Chirality : 0.043 0.245 1813 Planarity : 0.004 0.039 1833 Dihedral : 8.028 75.205 2123 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.04 % Allowed : 12.70 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1303 helix: 1.80 (0.20), residues: 719 sheet: -0.92 (0.43), residues: 130 loop : -1.94 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 209 HIS 0.003 0.001 HIS A 553 PHE 0.030 0.001 PHE A 302 TYR 0.014 0.001 TYR A 569 ARG 0.009 0.000 ARG A 391 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 12) link_NAG-ASN : angle 2.22935 ( 36) link_BETA1-4 : bond 0.00262 ( 7) link_BETA1-4 : angle 1.57573 ( 21) hydrogen bonds : bond 0.03986 ( 545) hydrogen bonds : angle 3.79697 ( 1587) link_BETA1-6 : bond 0.00934 ( 1) link_BETA1-6 : angle 2.58577 ( 3) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.66306 ( 8) link_BETA1-3 : bond 0.00730 ( 1) link_BETA1-3 : angle 1.38487 ( 3) covalent geometry : bond 0.00303 (11133) covalent geometry : angle 0.59072 (15185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6378.12 seconds wall clock time: 117 minutes 13.31 seconds (7033.31 seconds total)