Starting phenix.real_space_refine on Sat Aug 23 12:37:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmz_61616/08_2025/9jmz_61616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmz_61616/08_2025/9jmz_61616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jmz_61616/08_2025/9jmz_61616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmz_61616/08_2025/9jmz_61616.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmz_61616/08_2025/9jmz_61616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmz_61616/08_2025/9jmz_61616.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 7520 2.51 5 N 2054 2.21 5 O 2358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12001 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3897 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 19, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3892 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 19, 'TRANS': 466} Chain breaks: 1 Chain: "C" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3892 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 19, 'TRANS': 466} Chain breaks: 1 Chain: "D" 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: "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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'GAL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" 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: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SIA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.00, per 1000 atoms: 0.25 Number of scatterers: 12001 At special positions: 0 Unit cell: (90.39, 86.94, 153.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 2358 8.00 N 2054 7.00 C 7520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " GAL F 2 " " NAG G 1 " - " GAL G 2 " " NAG H 1 " - " GAL H 2 " BETA2-3 " GAL F 2 " - " SIA F 3 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL G 2 " - " SIA G 3 " " GAL H 2 " - " SIA H 3 " NAG-ASN " NAG A 601 " - " ASN A 165 " " NAG A 602 " - " ASN A 11 " " NAG A 603 " - " ASN A 23 " " NAG A 604 " - " ASN A 286 " " NAG B 601 " - " ASN B 11 " " NAG B 602 " - " ASN B 286 " " NAG C 601 " - " ASN C 165 " " NAG C 602 " - " ASN C 23 " " NAG C 603 " - " ASN C 286 " " NAG D 1 " - " ASN B 165 " " NAG E 1 " - " ASN B 23 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 534.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 33 sheets defined 27.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.541A pdb=" N TRP A 122 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 Processing helix chain 'A' and resid 366 through 387 removed outlier: 3.622A pdb=" N THR A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 452 removed outlier: 3.965A pdb=" N ASP A 438 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N HIS A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 487 through 499 removed outlier: 3.868A pdb=" N TYR A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLU A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 97 through 105 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.573A pdb=" N TRP B 122 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.867A pdb=" N GLU B 340 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 366 through 387 removed outlier: 3.570A pdb=" N THR B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 456 removed outlier: 3.599A pdb=" N ASP B 438 " --> pdb=" O GLU B 434 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 499 removed outlier: 4.151A pdb=" N TYR B 491 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLU B 494 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.729A pdb=" N TRP C 122 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 366 through 387 removed outlier: 3.736A pdb=" N LYS C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 452 removed outlier: 3.534A pdb=" N GLU C 407 " --> pdb=" O GLU C 403 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 487 through 499 removed outlier: 4.235A pdb=" N TYR C 491 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLU C 494 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.516A pdb=" N GLY A 352 " --> pdb=" O GLY A 6 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 356 " --> pdb=" O GLN A 2 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 4.026A pdb=" N GLU A 14 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.838A pdb=" N LEU A 41 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N CYS A 274 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.693A pdb=" N LEU A 50 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 79 " --> pdb=" O MET A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.680A pdb=" N ARG A 225 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 171 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU A 175 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR A 252 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.680A pdb=" N ARG A 225 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU A 175 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 177 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 132 through 137 removed outlier: 4.746A pdb=" N CYS A 135 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 160 through 165 Processing sheet with id=AB2, first strand: chain 'A' and resid 283 through 285 removed outlier: 3.503A pdb=" N ILE A 285 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N CYS A 278 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 393 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.604A pdb=" N GLY B 352 " --> pdb=" O GLY B 6 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 356 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 3 " --> pdb=" O PHE B 467 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AB7, first strand: chain 'B' and resid 41 through 44 removed outlier: 7.010A pdb=" N LEU B 41 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N CYS B 274 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.485A pdb=" N LEU B 50 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 79 " --> pdb=" O MET B 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.963A pdb=" N SER B 94 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N TRP B 230 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 225 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP B 171 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU B 175 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR B 252 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 257 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N HIS B 110 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.963A pdb=" N SER B 94 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N TRP B 230 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 225 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU B 175 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 177 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 132 through 137 removed outlier: 4.845A pdb=" N CYS B 135 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AC4, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.723A pdb=" N CYS B 278 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 393 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 361 through 365 removed outlier: 3.641A pdb=" N GLY C 352 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS C 4 " --> pdb=" O HIS C 354 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C 356 " --> pdb=" O GLN C 2 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AC7, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AC8, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC9, first strand: chain 'C' and resid 41 through 44 removed outlier: 8.758A pdb=" N LEU C 41 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N THR C 276 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ASP C 43 " --> pdb=" O THR C 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.541A pdb=" N LEU C 50 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.954A pdb=" N SER C 94 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N TRP C 230 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 225 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 171 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU C 175 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C 252 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.954A pdb=" N SER C 94 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N TRP C 230 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 225 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU C 175 " --> pdb=" O PRO C 250 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 132 through 137 removed outlier: 4.734A pdb=" N CYS C 135 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 160 through 165 removed outlier: 3.600A pdb=" N ILE C 162 " --> pdb=" O PHE C 241 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 283 through 285 removed outlier: 4.159A pdb=" N CYS C 278 " --> pdb=" O ILE C 285 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1383 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: 2.21 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3951 1.34 - 1.47: 2928 1.47 - 1.59: 5287 1.59 - 1.71: 0 1.71 - 1.83: 102 Bond restraints: 12268 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.78e+00 bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C1 NAG C 603 " pdb=" O5 NAG C 603 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C3 GAL H 2 " pdb=" O3 GAL H 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 ... (remaining 12263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 16532 3.32 - 6.63: 70 6.63 - 9.95: 10 9.95 - 13.26: 3 13.26 - 16.58: 1 Bond angle restraints: 16616 Sorted by residual: angle pdb=" CA LEU A 453 " pdb=" CB LEU A 453 " pdb=" CG LEU A 453 " ideal model delta sigma weight residual 116.30 132.88 -16.58 3.50e+00 8.16e-02 2.24e+01 angle pdb=" CB MET A 388 " pdb=" CG MET A 388 " pdb=" SD MET A 388 " ideal model delta sigma weight residual 112.70 125.83 -13.13 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CB LYS A 450 " pdb=" CG LYS A 450 " pdb=" CD LYS A 450 " ideal model delta sigma weight residual 111.30 119.54 -8.24 2.30e+00 1.89e-01 1.28e+01 angle pdb=" CA ARG C 72 " pdb=" CB ARG C 72 " pdb=" CG ARG C 72 " ideal model delta sigma weight residual 114.10 121.19 -7.09 2.00e+00 2.50e-01 1.26e+01 angle pdb=" CA LYS A 450 " pdb=" CB LYS A 450 " pdb=" CG LYS A 450 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.17e+01 ... (remaining 16611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 6869 17.03 - 34.06: 622 34.06 - 51.10: 141 51.10 - 68.13: 48 68.13 - 85.16: 15 Dihedral angle restraints: 7695 sinusoidal: 3456 harmonic: 4239 Sorted by residual: dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual -86.00 -17.32 -68.68 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS C 42 " pdb=" SG CYS C 42 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual -86.00 -28.10 -57.90 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS B 67 " pdb=" CB CYS B 67 " ideal model delta sinusoidal sigma weight residual 93.00 141.96 -48.96 1 1.00e+01 1.00e-02 3.30e+01 ... (remaining 7692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 1820 0.170 - 0.340: 7 0.340 - 0.509: 4 0.509 - 0.679: 1 0.679 - 0.849: 1 Chirality restraints: 1833 Sorted by residual: chirality pdb=" C2 SIA F 3 " pdb=" O3 GAL F 2 " pdb=" C1 SIA F 3 " pdb=" O6 SIA F 3 " both_signs ideal model delta sigma weight residual False -2.50 -3.35 0.85 2.00e-02 2.50e+03 1.80e+03 chirality pdb=" C2 SIA G 3 " pdb=" O3 GAL G 2 " pdb=" C1 SIA G 3 " pdb=" O6 SIA G 3 " both_signs ideal model delta sigma weight residual False -2.50 -3.03 0.53 2.00e-02 2.50e+03 7.10e+02 chirality pdb=" C2 SIA H 3 " pdb=" O3 GAL H 2 " pdb=" C1 SIA H 3 " pdb=" O6 SIA H 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.97 0.47 2.00e-02 2.50e+03 5.45e+02 ... (remaining 1830 not shown) Planarity restraints: 2155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " 0.038 2.00e-02 2.50e+03 3.50e-02 1.53e+01 pdb=" CG ASN B 165 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 23 " 0.025 2.00e-02 2.50e+03 2.54e-02 8.06e+00 pdb=" CG ASN B 23 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 23 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 23 " -0.028 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 23 " -0.020 2.00e-02 2.50e+03 1.99e-02 4.93e+00 pdb=" CG ASN A 23 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 23 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 23 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " -0.018 2.00e-02 2.50e+03 ... (remaining 2152 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 567 2.72 - 3.27: 11265 3.27 - 3.81: 18881 3.81 - 4.36: 22354 4.36 - 4.90: 39388 Nonbonded interactions: 92455 Sorted by model distance: nonbonded pdb=" OD1 ASN B 286 " pdb=" N2 NAG B 602 " model vdw 2.176 3.120 nonbonded pdb=" O LYS A 445 " pdb=" NZ LYS A 445 " model vdw 2.214 3.120 nonbonded pdb=" O LYS C 450 " pdb=" NZ LYS C 450 " model vdw 2.218 3.120 nonbonded pdb=" OG1 THR A 18 " pdb=" OE1 GLU A 21 " model vdw 2.226 3.040 nonbonded pdb=" N GLU B 270 " pdb=" OE1 GLU B 270 " model vdw 2.229 3.120 ... (remaining 92450 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 'A' and (resid 1 through 320 or resid 335 through 602)) selection = chain 'B' selection = (chain 'C' and resid 1 through 602) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.370 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 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 : 0.004 0.213 12305 Z= 0.187 Angle : 0.899 29.071 16709 Z= 0.374 Chirality : 0.054 0.849 1833 Planarity : 0.003 0.035 2144 Dihedral : 14.151 85.161 4921 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.78 % Allowed : 15.11 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.22), residues: 1447 helix: 2.33 (0.27), residues: 371 sheet: 0.83 (0.32), residues: 223 loop : -0.81 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 435 TYR 0.008 0.001 TYR B 271 PHE 0.022 0.001 PHE A 469 TRP 0.006 0.000 TRP B 343 HIS 0.004 0.001 HIS B 273 Details of bonding type rmsd covalent geometry : bond 0.00324 (12268) covalent geometry : angle 0.64953 (16616) SS BOND : bond 0.00121 ( 18) SS BOND : angle 1.20373 ( 36) hydrogen bonds : bond 0.17859 ( 458) hydrogen bonds : angle 7.11327 ( 1383) link_BETA1-4 : bond 0.02639 ( 5) link_BETA1-4 : angle 10.05819 ( 15) link_BETA2-3 : bond 0.12563 ( 3) link_BETA2-3 : angle 19.65612 ( 9) link_NAG-ASN : bond 0.00810 ( 11) link_NAG-ASN : angle 6.60433 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 445 LYS cc_start: 0.9608 (tppp) cc_final: 0.9386 (tppp) outliers start: 10 outliers final: 9 residues processed: 68 average time/residue: 0.5149 time to fit residues: 38.5221 Evaluate side-chains 67 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 GLN C 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.050899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.035405 restraints weight = 46894.205| |-----------------------------------------------------------------------------| r_work (start): 0.2475 rms_B_bonded: 4.50 r_work: 0.2312 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12305 Z= 0.128 Angle : 0.640 16.243 16709 Z= 0.304 Chirality : 0.044 0.228 1833 Planarity : 0.003 0.033 2144 Dihedral : 8.380 79.689 2090 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.26 % Allowed : 12.62 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.22), residues: 1447 helix: 2.34 (0.28), residues: 374 sheet: 1.03 (0.32), residues: 230 loop : -0.84 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 435 TYR 0.010 0.001 TYR B 353 PHE 0.016 0.001 PHE B 70 TRP 0.005 0.001 TRP B 343 HIS 0.003 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00279 (12268) covalent geometry : angle 0.57786 (16616) SS BOND : bond 0.00148 ( 18) SS BOND : angle 0.91482 ( 36) hydrogen bonds : bond 0.05583 ( 458) hydrogen bonds : angle 5.31427 ( 1383) link_BETA1-4 : bond 0.00272 ( 5) link_BETA1-4 : angle 2.21116 ( 15) link_BETA2-3 : bond 0.00443 ( 3) link_BETA2-3 : angle 4.83940 ( 9) link_NAG-ASN : bond 0.00927 ( 11) link_NAG-ASN : angle 5.45715 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.9621 (tppp) cc_final: 0.9226 (tptp) REVERT: C 14 GLU cc_start: 0.8398 (mp0) cc_final: 0.8128 (mp0) REVERT: C 445 LYS cc_start: 0.9579 (tppp) cc_final: 0.9265 (tppp) outliers start: 29 outliers final: 14 residues processed: 80 average time/residue: 0.4190 time to fit residues: 37.2461 Evaluate side-chains 68 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 446 ASN Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 457 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN A 354 HIS A 359 GLN C 355 HIS C 440 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.048239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.032672 restraints weight = 48682.208| |-----------------------------------------------------------------------------| r_work (start): 0.2406 rms_B_bonded: 4.54 r_work: 0.2240 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12305 Z= 0.278 Angle : 0.703 16.889 16709 Z= 0.339 Chirality : 0.044 0.258 1833 Planarity : 0.004 0.039 2144 Dihedral : 7.704 70.134 2085 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.41 % Allowed : 13.24 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.22), residues: 1447 helix: 2.19 (0.28), residues: 374 sheet: 0.85 (0.32), residues: 240 loop : -1.08 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 452 TYR 0.009 0.001 TYR B 353 PHE 0.020 0.002 PHE A 439 TRP 0.006 0.001 TRP C 421 HIS 0.010 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00644 (12268) covalent geometry : angle 0.65132 (16616) SS BOND : bond 0.00349 ( 18) SS BOND : angle 0.92547 ( 36) hydrogen bonds : bond 0.06236 ( 458) hydrogen bonds : angle 5.14943 ( 1383) link_BETA1-4 : bond 0.00201 ( 5) link_BETA1-4 : angle 2.12954 ( 15) link_BETA2-3 : bond 0.00614 ( 3) link_BETA2-3 : angle 4.42819 ( 9) link_NAG-ASN : bond 0.00736 ( 11) link_NAG-ASN : angle 5.30981 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.9652 (tppp) cc_final: 0.9206 (tptp) REVERT: B 346 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.8411 (tmm) REVERT: B 413 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8926 (ttt) REVERT: C 14 GLU cc_start: 0.8733 (mp0) cc_final: 0.8378 (mp0) REVERT: C 445 LYS cc_start: 0.9599 (tppp) cc_final: 0.9279 (tppp) outliers start: 31 outliers final: 10 residues processed: 79 average time/residue: 0.4782 time to fit residues: 41.6436 Evaluate side-chains 67 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 367 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 33 optimal weight: 0.0870 chunk 81 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 HIS ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.050097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.034605 restraints weight = 47954.827| |-----------------------------------------------------------------------------| r_work (start): 0.2472 rms_B_bonded: 4.56 r_work: 0.2305 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12305 Z= 0.102 Angle : 0.606 17.564 16709 Z= 0.285 Chirality : 0.043 0.223 1833 Planarity : 0.003 0.032 2144 Dihedral : 7.295 71.576 2085 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.18 % Allowed : 13.40 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.22), residues: 1447 helix: 2.35 (0.28), residues: 374 sheet: 0.73 (0.31), residues: 260 loop : -0.92 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 456 TYR 0.008 0.001 TYR A 271 PHE 0.018 0.001 PHE A 469 TRP 0.004 0.000 TRP B 343 HIS 0.005 0.000 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00204 (12268) covalent geometry : angle 0.54934 (16616) SS BOND : bond 0.00126 ( 18) SS BOND : angle 0.85965 ( 36) hydrogen bonds : bond 0.05175 ( 458) hydrogen bonds : angle 4.75847 ( 1383) link_BETA1-4 : bond 0.00403 ( 5) link_BETA1-4 : angle 2.27732 ( 15) link_BETA2-3 : bond 0.00144 ( 3) link_BETA2-3 : angle 3.49659 ( 9) link_NAG-ASN : bond 0.00836 ( 11) link_NAG-ASN : angle 5.22335 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.9654 (tppp) cc_final: 0.9210 (tptp) REVERT: A 455 LEU cc_start: 0.9137 (mm) cc_final: 0.8845 (pp) REVERT: B 289 MET cc_start: 0.9562 (mmm) cc_final: 0.9250 (mmp) REVERT: B 346 MET cc_start: 0.9304 (ppp) cc_final: 0.8421 (tmm) REVERT: B 413 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8910 (tpt) REVERT: C 14 GLU cc_start: 0.8735 (mp0) cc_final: 0.8341 (mp0) REVERT: C 445 LYS cc_start: 0.9608 (tppp) cc_final: 0.9271 (tppp) outliers start: 28 outliers final: 8 residues processed: 78 average time/residue: 0.4165 time to fit residues: 36.1245 Evaluate side-chains 63 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 453 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 108 optimal weight: 0.0670 chunk 83 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 1.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.049647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.033895 restraints weight = 48555.700| |-----------------------------------------------------------------------------| r_work (start): 0.2451 rms_B_bonded: 4.61 r_work: 0.2286 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12305 Z= 0.139 Angle : 0.605 15.984 16709 Z= 0.286 Chirality : 0.043 0.222 1833 Planarity : 0.003 0.034 2144 Dihedral : 7.130 69.591 2083 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.87 % Allowed : 13.86 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.22), residues: 1447 helix: 2.33 (0.28), residues: 374 sheet: 1.05 (0.32), residues: 240 loop : -0.95 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 482 TYR 0.008 0.001 TYR B 191 PHE 0.018 0.001 PHE B 70 TRP 0.003 0.000 TRP C 421 HIS 0.006 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00317 (12268) covalent geometry : angle 0.55041 (16616) SS BOND : bond 0.00257 ( 18) SS BOND : angle 1.06076 ( 36) hydrogen bonds : bond 0.05189 ( 458) hydrogen bonds : angle 4.81353 ( 1383) link_BETA1-4 : bond 0.00202 ( 5) link_BETA1-4 : angle 2.14491 ( 15) link_BETA2-3 : bond 0.00355 ( 3) link_BETA2-3 : angle 3.50585 ( 9) link_NAG-ASN : bond 0.00693 ( 11) link_NAG-ASN : angle 5.08662 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.9666 (tppp) cc_final: 0.9219 (tptp) REVERT: A 455 LEU cc_start: 0.9154 (mm) cc_final: 0.8841 (pp) REVERT: B 289 MET cc_start: 0.9564 (mmm) cc_final: 0.9264 (mmp) REVERT: B 346 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8439 (tmm) REVERT: C 14 GLU cc_start: 0.8787 (mp0) cc_final: 0.8368 (mp0) REVERT: C 445 LYS cc_start: 0.9603 (tppp) cc_final: 0.9281 (tppp) outliers start: 24 outliers final: 11 residues processed: 69 average time/residue: 0.4633 time to fit residues: 35.2606 Evaluate side-chains 65 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN C 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.048127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.032371 restraints weight = 49079.378| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 4.59 r_work: 0.2231 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12305 Z= 0.248 Angle : 0.666 16.591 16709 Z= 0.322 Chirality : 0.044 0.250 1833 Planarity : 0.003 0.036 2144 Dihedral : 7.142 67.648 2083 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.26 % Allowed : 13.55 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.22), residues: 1447 helix: 2.22 (0.28), residues: 374 sheet: 1.01 (0.32), residues: 250 loop : -1.06 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 482 TYR 0.009 0.001 TYR B 353 PHE 0.016 0.002 PHE A 439 TRP 0.006 0.001 TRP C 421 HIS 0.004 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00577 (12268) covalent geometry : angle 0.61827 (16616) SS BOND : bond 0.00242 ( 18) SS BOND : angle 1.16236 ( 36) hydrogen bonds : bond 0.05881 ( 458) hydrogen bonds : angle 4.95127 ( 1383) link_BETA1-4 : bond 0.00151 ( 5) link_BETA1-4 : angle 2.10065 ( 15) link_BETA2-3 : bond 0.00719 ( 3) link_BETA2-3 : angle 3.61755 ( 9) link_NAG-ASN : bond 0.00645 ( 11) link_NAG-ASN : angle 5.03426 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.9668 (tppp) cc_final: 0.9195 (tptp) REVERT: B 289 MET cc_start: 0.9576 (mmm) cc_final: 0.9229 (mmp) REVERT: B 346 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8357 (tmm) REVERT: C 14 GLU cc_start: 0.8917 (mp0) cc_final: 0.8449 (mp0) REVERT: C 445 LYS cc_start: 0.9639 (tppp) cc_final: 0.9339 (tppp) outliers start: 29 outliers final: 14 residues processed: 80 average time/residue: 0.4137 time to fit residues: 36.9806 Evaluate side-chains 68 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.2942 r_free = 0.2942 target = 0.049179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.033697 restraints weight = 47613.531| |-----------------------------------------------------------------------------| r_work (start): 0.2444 rms_B_bonded: 4.52 r_work: 0.2277 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12305 Z= 0.118 Angle : 0.622 18.228 16709 Z= 0.292 Chirality : 0.044 0.410 1833 Planarity : 0.003 0.034 2144 Dihedral : 7.024 68.806 2083 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.71 % Allowed : 14.41 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.22), residues: 1447 helix: 2.28 (0.28), residues: 374 sheet: 0.73 (0.31), residues: 256 loop : -0.99 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 482 TYR 0.008 0.001 TYR C 271 PHE 0.012 0.001 PHE A 439 TRP 0.003 0.000 TRP B 343 HIS 0.002 0.000 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00259 (12268) covalent geometry : angle 0.56956 (16616) SS BOND : bond 0.00146 ( 18) SS BOND : angle 0.99871 ( 36) hydrogen bonds : bond 0.05279 ( 458) hydrogen bonds : angle 4.76588 ( 1383) link_BETA1-4 : bond 0.00391 ( 5) link_BETA1-4 : angle 2.08717 ( 15) link_BETA2-3 : bond 0.00338 ( 3) link_BETA2-3 : angle 3.21993 ( 9) link_NAG-ASN : bond 0.00675 ( 11) link_NAG-ASN : angle 5.17921 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 280 THR cc_start: 0.9575 (OUTLIER) cc_final: 0.9106 (p) REVERT: A 445 LYS cc_start: 0.9665 (tppp) cc_final: 0.9192 (tptp) REVERT: A 455 LEU cc_start: 0.9183 (mm) cc_final: 0.8827 (pp) REVERT: B 289 MET cc_start: 0.9570 (mmm) cc_final: 0.9190 (mmp) REVERT: B 346 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8377 (tmm) REVERT: C 14 GLU cc_start: 0.8916 (mp0) cc_final: 0.8457 (mp0) REVERT: C 445 LYS cc_start: 0.9625 (tppp) cc_final: 0.9330 (tppp) outliers start: 22 outliers final: 14 residues processed: 73 average time/residue: 0.4421 time to fit residues: 35.8363 Evaluate side-chains 70 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN C 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.048233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.032602 restraints weight = 48810.166| |-----------------------------------------------------------------------------| r_work (start): 0.2409 rms_B_bonded: 4.54 r_work: 0.2241 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12305 Z= 0.225 Angle : 0.667 16.919 16709 Z= 0.319 Chirality : 0.044 0.266 1833 Planarity : 0.003 0.036 2144 Dihedral : 7.045 67.532 2083 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.40 % Allowed : 14.88 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1447 helix: 2.14 (0.27), residues: 374 sheet: 0.75 (0.31), residues: 266 loop : -1.05 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 452 TYR 0.008 0.001 TYR B 353 PHE 0.025 0.002 PHE B 70 TRP 0.005 0.001 TRP C 122 HIS 0.003 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00522 (12268) covalent geometry : angle 0.62024 (16616) SS BOND : bond 0.00222 ( 18) SS BOND : angle 1.31027 ( 36) hydrogen bonds : bond 0.05673 ( 458) hydrogen bonds : angle 4.89117 ( 1383) link_BETA1-4 : bond 0.00192 ( 5) link_BETA1-4 : angle 2.01961 ( 15) link_BETA2-3 : bond 0.00612 ( 3) link_BETA2-3 : angle 3.35520 ( 9) link_NAG-ASN : bond 0.00599 ( 11) link_NAG-ASN : angle 4.96883 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 280 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9096 (p) REVERT: A 445 LYS cc_start: 0.9670 (tppp) cc_final: 0.9204 (tptp) REVERT: A 455 LEU cc_start: 0.9206 (mm) cc_final: 0.8829 (pp) REVERT: B 289 MET cc_start: 0.9579 (mmm) cc_final: 0.9235 (mmp) REVERT: B 340 GLU cc_start: 0.9116 (tp30) cc_final: 0.8653 (tm-30) REVERT: B 346 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8416 (tmm) REVERT: C 14 GLU cc_start: 0.8968 (mp0) cc_final: 0.8563 (mp0) REVERT: C 445 LYS cc_start: 0.9636 (tppp) cc_final: 0.9307 (tppp) outliers start: 18 outliers final: 14 residues processed: 71 average time/residue: 0.4370 time to fit residues: 34.5803 Evaluate side-chains 70 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.2937 r_free = 0.2937 target = 0.048929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.033491 restraints weight = 47448.157| |-----------------------------------------------------------------------------| r_work (start): 0.2437 rms_B_bonded: 4.50 r_work: 0.2271 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12305 Z= 0.135 Angle : 0.640 17.008 16709 Z= 0.302 Chirality : 0.043 0.244 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.950 68.415 2083 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.56 % Allowed : 14.64 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.22), residues: 1447 helix: 2.14 (0.27), residues: 374 sheet: 0.77 (0.31), residues: 267 loop : -1.01 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 482 TYR 0.008 0.001 TYR B 353 PHE 0.013 0.001 PHE A 439 TRP 0.003 0.000 TRP A 343 HIS 0.002 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00305 (12268) covalent geometry : angle 0.59316 (16616) SS BOND : bond 0.00130 ( 18) SS BOND : angle 1.13517 ( 36) hydrogen bonds : bond 0.05383 ( 458) hydrogen bonds : angle 4.78754 ( 1383) link_BETA1-4 : bond 0.00228 ( 5) link_BETA1-4 : angle 2.03581 ( 15) link_BETA2-3 : bond 0.00356 ( 3) link_BETA2-3 : angle 3.14383 ( 9) link_NAG-ASN : bond 0.00652 ( 11) link_NAG-ASN : angle 4.92615 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 280 THR cc_start: 0.9575 (OUTLIER) cc_final: 0.9109 (p) REVERT: A 445 LYS cc_start: 0.9659 (tppp) cc_final: 0.9192 (tptp) REVERT: A 455 LEU cc_start: 0.9207 (mm) cc_final: 0.8827 (pp) REVERT: B 289 MET cc_start: 0.9568 (mmm) cc_final: 0.9205 (mmp) REVERT: B 340 GLU cc_start: 0.9112 (tp30) cc_final: 0.8642 (tm-30) REVERT: B 346 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8277 (tmm) REVERT: C 14 GLU cc_start: 0.8960 (mp0) cc_final: 0.8553 (mp0) REVERT: C 413 MET cc_start: 0.8922 (tpt) cc_final: 0.8568 (tpt) REVERT: C 445 LYS cc_start: 0.9623 (tppp) cc_final: 0.9308 (tppp) outliers start: 20 outliers final: 15 residues processed: 73 average time/residue: 0.4466 time to fit residues: 36.3125 Evaluate side-chains 72 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 0.0570 chunk 112 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 446 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.033863 restraints weight = 47974.092| |-----------------------------------------------------------------------------| r_work (start): 0.2454 rms_B_bonded: 4.57 r_work: 0.2289 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12305 Z= 0.117 Angle : 0.608 15.962 16709 Z= 0.290 Chirality : 0.043 0.229 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.751 68.559 2083 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.32 % Allowed : 14.95 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.22), residues: 1447 helix: 2.15 (0.27), residues: 378 sheet: 0.88 (0.31), residues: 266 loop : -1.00 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 435 TYR 0.007 0.001 TYR C 271 PHE 0.024 0.001 PHE B 70 TRP 0.003 0.000 TRP B 343 HIS 0.002 0.000 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00261 (12268) covalent geometry : angle 0.56057 (16616) SS BOND : bond 0.00123 ( 18) SS BOND : angle 1.07154 ( 36) hydrogen bonds : bond 0.05056 ( 458) hydrogen bonds : angle 4.70490 ( 1383) link_BETA1-4 : bond 0.00224 ( 5) link_BETA1-4 : angle 2.01029 ( 15) link_BETA2-3 : bond 0.00389 ( 3) link_BETA2-3 : angle 3.07075 ( 9) link_NAG-ASN : bond 0.00652 ( 11) link_NAG-ASN : angle 4.85467 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 280 THR cc_start: 0.9549 (OUTLIER) cc_final: 0.9104 (p) REVERT: A 445 LYS cc_start: 0.9641 (tppp) cc_final: 0.9175 (tptp) REVERT: A 455 LEU cc_start: 0.9149 (mm) cc_final: 0.8792 (pp) REVERT: B 289 MET cc_start: 0.9544 (mmm) cc_final: 0.9178 (mmp) REVERT: B 340 GLU cc_start: 0.9058 (tp30) cc_final: 0.8584 (tm-30) REVERT: B 346 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8355 (tmm) REVERT: C 14 GLU cc_start: 0.8938 (mp0) cc_final: 0.8531 (mp0) REVERT: C 413 MET cc_start: 0.8882 (tpt) cc_final: 0.8538 (tpt) REVERT: C 445 LYS cc_start: 0.9606 (tppp) cc_final: 0.9309 (tppp) outliers start: 17 outliers final: 13 residues processed: 73 average time/residue: 0.4192 time to fit residues: 34.0183 Evaluate side-chains 68 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 353 TYR Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 108 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 95 optimal weight: 30.0000 chunk 116 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 109 optimal weight: 0.0010 chunk 125 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 = 0.2961 r_free = 0.2961 target = 0.049747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.034292 restraints weight = 48108.216| |-----------------------------------------------------------------------------| r_work (start): 0.2463 rms_B_bonded: 4.53 r_work: 0.2298 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12305 Z= 0.114 Angle : 0.634 17.160 16709 Z= 0.297 Chirality : 0.043 0.228 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.608 68.569 2081 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.32 % Allowed : 14.95 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.22), residues: 1447 helix: 2.06 (0.27), residues: 378 sheet: 0.86 (0.32), residues: 256 loop : -0.92 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 452 TYR 0.007 0.001 TYR C 271 PHE 0.012 0.001 PHE A 439 TRP 0.003 0.000 TRP B 350 HIS 0.002 0.000 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00251 (12268) covalent geometry : angle 0.58965 (16616) SS BOND : bond 0.00106 ( 18) SS BOND : angle 1.00921 ( 36) hydrogen bonds : bond 0.04937 ( 458) hydrogen bonds : angle 4.67031 ( 1383) link_BETA1-4 : bond 0.00245 ( 5) link_BETA1-4 : angle 1.99812 ( 15) link_BETA2-3 : bond 0.00319 ( 3) link_BETA2-3 : angle 3.02278 ( 9) link_NAG-ASN : bond 0.00652 ( 11) link_NAG-ASN : angle 4.82189 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2644.17 seconds wall clock time: 46 minutes 6.70 seconds (2766.70 seconds total)