Starting phenix.real_space_refine on Tue Jun 10 21:55:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmz_61616/06_2025/9jmz_61616.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmz_61616/06_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_61616/06_2025/9jmz_61616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmz_61616/06_2025/9jmz_61616.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmz_61616/06_2025/9jmz_61616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmz_61616/06_2025/9jmz_61616.cif" } resolution = 2.91 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= 0.026 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.37, per 1000 atoms: 0.61 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.50 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: 3.59 Time building geometry restraints manager: 3.34 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 500 or resid 601 throug \ h 602)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 500 or resid 601 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.040 Find NCS groups from input model: 0.590 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:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.840 ------------------------------------------------------------------------------- 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 (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: 0.45 (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 TRP 0.006 0.000 TRP B 343 HIS 0.004 0.001 HIS B 273 PHE 0.022 0.001 PHE A 469 TYR 0.008 0.001 TYR B 271 ARG 0.005 0.000 ARG C 435 Details of bonding type rmsd 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) link_BETA1-4 : bond 0.02639 ( 5) link_BETA1-4 : angle 10.05819 ( 15) hydrogen bonds : bond 0.17859 ( 458) hydrogen bonds : angle 7.11327 ( 1383) SS BOND : bond 0.00121 ( 18) SS BOND : angle 1.20373 ( 36) covalent geometry : bond 0.00324 (12268) covalent geometry : angle 0.64953 (16616) *********************** 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 : 1.369 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: 1.2134 time to fit residues: 90.9650 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 : 1.578 ------------------------------------------------------------------------------- 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 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 130 optimal weight: 0.0970 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN C 218 GLN C 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.034202 restraints weight = 47746.293| |-----------------------------------------------------------------------------| r_work (start): 0.2437 rms_B_bonded: 4.60 r_work: 0.2272 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12305 Z= 0.182 Angle : 0.664 16.512 16709 Z= 0.317 Chirality : 0.044 0.242 1833 Planarity : 0.003 0.033 2144 Dihedral : 8.354 79.460 2090 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.34 % Allowed : 12.62 % Favored : 85.05 % 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: 0.40 (0.22), residues: 1447 helix: 2.28 (0.28), residues: 374 sheet: 0.89 (0.32), residues: 235 loop : -0.91 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 343 HIS 0.004 0.001 HIS A 8 PHE 0.016 0.001 PHE A 439 TYR 0.010 0.001 TYR C 353 ARG 0.005 0.000 ARG C 435 Details of bonding type rmsd link_BETA2-3 : bond 0.00800 ( 3) link_BETA2-3 : angle 4.67014 ( 9) link_NAG-ASN : bond 0.00884 ( 11) link_NAG-ASN : angle 5.51273 ( 33) link_BETA1-4 : bond 0.00291 ( 5) link_BETA1-4 : angle 2.11735 ( 15) hydrogen bonds : bond 0.05793 ( 458) hydrogen bonds : angle 5.28956 ( 1383) SS BOND : bond 0.00194 ( 18) SS BOND : angle 0.93629 ( 36) covalent geometry : bond 0.00414 (12268) covalent geometry : angle 0.60416 (16616) *********************** 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 88 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.9606 (tppp) cc_final: 0.9200 (tptp) REVERT: B 413 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8714 (tpt) REVERT: C 14 GLU cc_start: 0.8440 (mp0) cc_final: 0.8173 (mp0) REVERT: C 367 LYS cc_start: 0.9626 (OUTLIER) cc_final: 0.9396 (pmmt) REVERT: C 445 LYS cc_start: 0.9575 (tppp) cc_final: 0.9263 (tppp) outliers start: 30 outliers final: 11 residues processed: 83 average time/residue: 0.9944 time to fit residues: 92.2849 Evaluate side-chains 67 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 367 LYS Chi-restraints excluded: chain C residue 453 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.0670 chunk 96 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 overall best weight: 3.1724 ------------------------------------------------------------------------------- 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 A 454 GLN C 354 HIS C 355 HIS C 440 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.048868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.033307 restraints weight = 47944.503| |-----------------------------------------------------------------------------| r_work (start): 0.2427 rms_B_bonded: 4.53 r_work: 0.2259 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12305 Z= 0.200 Angle : 0.647 16.807 16709 Z= 0.309 Chirality : 0.044 0.246 1833 Planarity : 0.003 0.032 2144 Dihedral : 7.490 69.286 2085 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.34 % Allowed : 13.01 % Favored : 84.66 % 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: 0.29 (0.22), residues: 1447 helix: 2.28 (0.28), residues: 374 sheet: 0.62 (0.31), residues: 260 loop : -1.01 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 421 HIS 0.008 0.001 HIS C 355 PHE 0.016 0.001 PHE A 439 TYR 0.009 0.001 TYR B 353 ARG 0.003 0.000 ARG C 72 Details of bonding type rmsd link_BETA2-3 : bond 0.00559 ( 3) link_BETA2-3 : angle 4.12311 ( 9) link_NAG-ASN : bond 0.00761 ( 11) link_NAG-ASN : angle 5.25333 ( 33) link_BETA1-4 : bond 0.00212 ( 5) link_BETA1-4 : angle 2.20073 ( 15) hydrogen bonds : bond 0.05873 ( 458) hydrogen bonds : angle 4.99410 ( 1383) SS BOND : bond 0.00252 ( 18) SS BOND : angle 0.93905 ( 36) covalent geometry : bond 0.00459 (12268) covalent geometry : angle 0.59196 (16616) *********************** 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 85 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 346 MET cc_start: 0.8958 (ttp) cc_final: 0.8737 (ttp) REVERT: A 445 LYS cc_start: 0.9652 (tppp) cc_final: 0.9210 (tptp) REVERT: B 346 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8392 (tmm) REVERT: B 413 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8645 (tpt) REVERT: C 14 GLU cc_start: 0.8734 (mp0) cc_final: 0.8374 (mp0) REVERT: C 445 LYS cc_start: 0.9585 (tppp) cc_final: 0.9260 (tppp) outliers start: 30 outliers final: 13 residues processed: 77 average time/residue: 1.0849 time to fit residues: 92.9518 Evaluate side-chains 69 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET 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 353 TYR 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 449 ASP Chi-restraints excluded: chain C residue 453 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 38 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.047228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.031529 restraints weight = 48825.349| |-----------------------------------------------------------------------------| r_work (start): 0.2370 rms_B_bonded: 4.53 r_work: 0.2201 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 12305 Z= 0.299 Angle : 0.720 16.923 16709 Z= 0.350 Chirality : 0.045 0.260 1833 Planarity : 0.004 0.042 2144 Dihedral : 7.457 68.987 2085 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.04 % Allowed : 13.16 % 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 (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: 0.09 (0.22), residues: 1447 helix: 2.07 (0.28), residues: 374 sheet: 0.85 (0.32), residues: 246 loop : -1.22 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 122 HIS 0.011 0.001 HIS C 355 PHE 0.022 0.002 PHE A 439 TYR 0.010 0.001 TYR B 353 ARG 0.006 0.001 ARG C 452 Details of bonding type rmsd link_BETA2-3 : bond 0.01060 ( 3) link_BETA2-3 : angle 3.87162 ( 9) link_NAG-ASN : bond 0.00709 ( 11) link_NAG-ASN : angle 5.21616 ( 33) link_BETA1-4 : bond 0.00397 ( 5) link_BETA1-4 : angle 2.14254 ( 15) hydrogen bonds : bond 0.06535 ( 458) hydrogen bonds : angle 5.08049 ( 1383) SS BOND : bond 0.00313 ( 18) SS BOND : angle 0.96269 ( 36) covalent geometry : bond 0.00694 (12268) covalent geometry : angle 0.67251 (16616) *********************** 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 97 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 58 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 LYS cc_start: 0.9656 (tppp) cc_final: 0.9188 (tptp) REVERT: B 346 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8240 (tmm) REVERT: B 413 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8858 (tpp) REVERT: C 14 GLU cc_start: 0.8932 (mp0) cc_final: 0.8493 (mp0) REVERT: C 265 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8549 (tpt) REVERT: C 445 LYS cc_start: 0.9617 (tppp) cc_final: 0.9357 (tppp) outliers start: 39 outliers final: 18 residues processed: 87 average time/residue: 1.0093 time to fit residues: 97.9697 Evaluate side-chains 76 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 274 CYS 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 274 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 413 MET Chi-restraints excluded: chain B residue 477 CYS Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 477 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.2921 r_free = 0.2921 target = 0.048492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.033039 restraints weight = 47577.464| |-----------------------------------------------------------------------------| r_work (start): 0.2417 rms_B_bonded: 4.50 r_work: 0.2250 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1801 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 : 0.617 16.634 16709 Z= 0.295 Chirality : 0.044 0.266 1833 Planarity : 0.003 0.033 2144 Dihedral : 7.166 68.557 2085 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.65 % Allowed : 13.08 % 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 (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: 0.25 (0.22), residues: 1447 helix: 2.24 (0.28), residues: 374 sheet: 0.67 (0.31), residues: 266 loop : -1.08 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 60 HIS 0.005 0.001 HIS C 355 PHE 0.013 0.001 PHE A 439 TYR 0.008 0.001 TYR B 353 ARG 0.003 0.000 ARG C 435 Details of bonding type rmsd link_BETA2-3 : bond 0.00297 ( 3) link_BETA2-3 : angle 3.31050 ( 9) link_NAG-ASN : bond 0.00681 ( 11) link_NAG-ASN : angle 5.09783 ( 33) link_BETA1-4 : bond 0.00329 ( 5) link_BETA1-4 : angle 2.14451 ( 15) hydrogen bonds : bond 0.05647 ( 458) hydrogen bonds : angle 4.79456 ( 1383) SS BOND : bond 0.00182 ( 18) SS BOND : angle 1.00412 ( 36) covalent geometry : bond 0.00298 (12268) covalent geometry : angle 0.56514 (16616) *********************** 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 88 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 54 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.9659 (tppp) cc_final: 0.9191 (tptp) REVERT: B 346 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8285 (tmm) REVERT: B 413 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8753 (tpt) REVERT: C 14 GLU cc_start: 0.8916 (mp0) cc_final: 0.8446 (mp0) REVERT: C 51 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9115 (mm) REVERT: C 445 LYS cc_start: 0.9649 (tppp) cc_final: 0.9325 (tppp) outliers start: 34 outliers final: 14 residues processed: 80 average time/residue: 1.0153 time to fit residues: 91.0491 Evaluate side-chains 70 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU 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 274 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 413 MET Chi-restraints excluded: chain C residue 51 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 64 optimal weight: 0.0980 chunk 129 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.049080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.033600 restraints weight = 48049.041| |-----------------------------------------------------------------------------| r_work (start): 0.2437 rms_B_bonded: 4.52 r_work: 0.2270 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12305 Z= 0.109 Angle : 0.606 16.705 16709 Z= 0.287 Chirality : 0.044 0.440 1833 Planarity : 0.003 0.034 2144 Dihedral : 7.031 68.946 2085 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.49 % Allowed : 13.63 % 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 (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: 0.39 (0.22), residues: 1447 helix: 2.30 (0.27), residues: 374 sheet: 0.68 (0.30), residues: 280 loop : -0.95 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 343 HIS 0.006 0.000 HIS C 355 PHE 0.022 0.001 PHE B 70 TYR 0.008 0.001 TYR B 353 ARG 0.002 0.000 ARG C 435 Details of bonding type rmsd link_BETA2-3 : bond 0.00336 ( 3) link_BETA2-3 : angle 3.22197 ( 9) link_NAG-ASN : bond 0.00662 ( 11) link_NAG-ASN : angle 5.11585 ( 33) link_BETA1-4 : bond 0.00352 ( 5) link_BETA1-4 : angle 2.11141 ( 15) hydrogen bonds : bond 0.05226 ( 458) hydrogen bonds : angle 4.66531 ( 1383) SS BOND : bond 0.00160 ( 18) SS BOND : angle 0.88446 ( 36) covalent geometry : bond 0.00234 (12268) covalent geometry : angle 0.55351 (16616) *********************** 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 86 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: A 280 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.9137 (p) REVERT: A 445 LYS cc_start: 0.9656 (tppp) cc_final: 0.9173 (tptp) REVERT: B 338 PHE cc_start: 0.8506 (t80) cc_final: 0.8291 (t80) REVERT: B 346 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8330 (tmm) REVERT: B 413 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8904 (tpp) REVERT: C 14 GLU cc_start: 0.8928 (mp0) cc_final: 0.8519 (mp0) REVERT: C 445 LYS cc_start: 0.9627 (tppp) cc_final: 0.9305 (tppp) outliers start: 32 outliers final: 15 residues processed: 80 average time/residue: 0.9773 time to fit residues: 88.1977 Evaluate side-chains 70 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 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 274 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 413 MET Chi-restraints excluded: chain B residue 477 CYS 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 17 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.2936 r_free = 0.2936 target = 0.048952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.033355 restraints weight = 48069.035| |-----------------------------------------------------------------------------| r_work (start): 0.2432 rms_B_bonded: 4.53 r_work: 0.2267 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1908 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= 0.140 Angle : 0.612 16.670 16709 Z= 0.291 Chirality : 0.043 0.317 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.891 68.115 2083 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.10 % Allowed : 14.25 % Favored : 83.64 % 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: 0.39 (0.22), residues: 1447 helix: 2.27 (0.27), residues: 378 sheet: 0.73 (0.31), residues: 276 loop : -0.96 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 350 HIS 0.005 0.001 HIS C 355 PHE 0.012 0.001 PHE A 439 TYR 0.008 0.001 TYR B 353 ARG 0.002 0.000 ARG C 435 Details of bonding type rmsd link_BETA2-3 : bond 0.00409 ( 3) link_BETA2-3 : angle 3.21323 ( 9) link_NAG-ASN : bond 0.00658 ( 11) link_NAG-ASN : angle 4.86443 ( 33) link_BETA1-4 : bond 0.00197 ( 5) link_BETA1-4 : angle 2.05729 ( 15) hydrogen bonds : bond 0.05240 ( 458) hydrogen bonds : angle 4.67045 ( 1383) SS BOND : bond 0.00168 ( 18) SS BOND : angle 0.85336 ( 36) covalent geometry : bond 0.00319 (12268) covalent geometry : angle 0.56453 (16616) *********************** 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 80 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 280 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.9133 (p) REVERT: A 445 LYS cc_start: 0.9656 (tppp) cc_final: 0.9185 (tptp) REVERT: B 346 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8325 (tmm) REVERT: B 413 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8932 (tpp) REVERT: C 14 GLU cc_start: 0.8946 (mp0) cc_final: 0.8522 (mp0) REVERT: C 265 MET cc_start: 0.8895 (tpt) cc_final: 0.8536 (tpp) REVERT: C 445 LYS cc_start: 0.9630 (tppp) cc_final: 0.9342 (tppp) outliers start: 27 outliers final: 17 residues processed: 75 average time/residue: 1.1364 time to fit residues: 95.8593 Evaluate side-chains 73 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 274 CYS 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 274 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 413 MET 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 46 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN C 189 ASN C 218 GLN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.046957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.031391 restraints weight = 49573.763| |-----------------------------------------------------------------------------| r_work (start): 0.2363 rms_B_bonded: 4.52 r_work: 0.2195 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 12305 Z= 0.347 Angle : 0.745 17.235 16709 Z= 0.362 Chirality : 0.046 0.281 1833 Planarity : 0.004 0.041 2144 Dihedral : 7.054 66.407 2083 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.71 % Allowed : 14.80 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1447 helix: 2.00 (0.27), residues: 378 sheet: 0.59 (0.30), residues: 286 loop : -1.25 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 421 HIS 0.011 0.001 HIS C 355 PHE 0.025 0.002 PHE B 70 TYR 0.010 0.001 TYR B 164 ARG 0.008 0.001 ARG C 452 Details of bonding type rmsd link_BETA2-3 : bond 0.00986 ( 3) link_BETA2-3 : angle 3.57276 ( 9) link_NAG-ASN : bond 0.00613 ( 11) link_NAG-ASN : angle 4.91885 ( 33) link_BETA1-4 : bond 0.00401 ( 5) link_BETA1-4 : angle 2.14261 ( 15) hydrogen bonds : bond 0.06406 ( 458) hydrogen bonds : angle 5.06053 ( 1383) SS BOND : bond 0.00332 ( 18) SS BOND : angle 0.91579 ( 36) covalent geometry : bond 0.00799 (12268) covalent geometry : angle 0.70519 (16616) *********************** 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 78 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: A 445 LYS cc_start: 0.9671 (tppp) cc_final: 0.9160 (tptp) REVERT: B 346 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8276 (tmm) REVERT: B 413 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8933 (tpp) REVERT: C 14 GLU cc_start: 0.9048 (mp0) cc_final: 0.8575 (mp0) REVERT: C 445 LYS cc_start: 0.9656 (tppp) cc_final: 0.9447 (tppp) outliers start: 22 outliers final: 15 residues processed: 75 average time/residue: 1.0544 time to fit residues: 88.6235 Evaluate side-chains 71 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 280 THR Chi-restraints excluded: chain A residue 353 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain B residue 274 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 413 MET 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 477 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.2936 r_free = 0.2936 target = 0.048959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.033365 restraints weight = 47744.155| |-----------------------------------------------------------------------------| r_work (start): 0.2433 rms_B_bonded: 4.53 r_work: 0.2266 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12305 Z= 0.111 Angle : 0.635 17.455 16709 Z= 0.300 Chirality : 0.044 0.270 1833 Planarity : 0.003 0.033 2144 Dihedral : 6.879 70.605 2083 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.32 % Allowed : 15.42 % Favored : 83.26 % 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: 0.31 (0.22), residues: 1447 helix: 2.20 (0.27), residues: 374 sheet: 0.65 (0.31), residues: 277 loop : -0.98 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 343 HIS 0.003 0.001 HIS C 355 PHE 0.011 0.001 PHE A 439 TYR 0.010 0.001 TYR C 271 ARG 0.004 0.000 ARG A 452 Details of bonding type rmsd link_BETA2-3 : bond 0.00315 ( 3) link_BETA2-3 : angle 3.03827 ( 9) link_NAG-ASN : bond 0.00689 ( 11) link_NAG-ASN : angle 4.84572 ( 33) link_BETA1-4 : bond 0.00359 ( 5) link_BETA1-4 : angle 2.06731 ( 15) hydrogen bonds : bond 0.05379 ( 458) hydrogen bonds : angle 4.71448 ( 1383) SS BOND : bond 0.00141 ( 18) SS BOND : angle 0.89294 ( 36) covalent geometry : bond 0.00233 (12268) covalent geometry : angle 0.58989 (16616) *********************** 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 73 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 280 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9128 (p) REVERT: A 445 LYS cc_start: 0.9644 (tppp) cc_final: 0.9166 (tptp) REVERT: B 289 MET cc_start: 0.9141 (mmm) cc_final: 0.8283 (mmm) REVERT: B 340 GLU cc_start: 0.9095 (tp30) cc_final: 0.8642 (tm-30) REVERT: B 346 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8305 (tmm) REVERT: B 413 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8935 (tpp) REVERT: C 14 GLU cc_start: 0.8999 (mp0) cc_final: 0.8554 (mp0) REVERT: C 445 LYS cc_start: 0.9630 (tppp) cc_final: 0.9312 (tppp) outliers start: 17 outliers final: 13 residues processed: 70 average time/residue: 1.2882 time to fit residues: 99.8487 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 : 1.296 ------------------------------------------------------------------------------- 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 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 413 MET 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 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 98 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.048392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.032924 restraints weight = 47647.131| |-----------------------------------------------------------------------------| r_work (start): 0.2416 rms_B_bonded: 4.48 r_work: 0.2251 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12305 Z= 0.169 Angle : 0.628 16.477 16709 Z= 0.301 Chirality : 0.044 0.254 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.786 68.549 2083 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.48 % Allowed : 15.26 % Favored : 83.26 % 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: 0.27 (0.22), residues: 1447 helix: 2.19 (0.27), residues: 378 sheet: 0.71 (0.30), residues: 287 loop : -1.10 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 350 HIS 0.005 0.001 HIS C 355 PHE 0.025 0.001 PHE B 70 TYR 0.008 0.001 TYR B 353 ARG 0.002 0.000 ARG C 435 Details of bonding type rmsd link_BETA2-3 : bond 0.00555 ( 3) link_BETA2-3 : angle 3.15541 ( 9) link_NAG-ASN : bond 0.00592 ( 11) link_NAG-ASN : angle 4.79697 ( 33) link_BETA1-4 : bond 0.00184 ( 5) link_BETA1-4 : angle 2.00119 ( 15) hydrogen bonds : bond 0.05467 ( 458) hydrogen bonds : angle 4.80383 ( 1383) SS BOND : bond 0.00170 ( 18) SS BOND : angle 1.39498 ( 36) covalent geometry : bond 0.00389 (12268) covalent geometry : angle 0.58064 (16616) ********************** 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 73 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 280 THR cc_start: 0.9578 (OUTLIER) cc_final: 0.9113 (p) REVERT: A 445 LYS cc_start: 0.9650 (tppp) cc_final: 0.9167 (tptp) REVERT: B 289 MET cc_start: 0.9114 (mmm) cc_final: 0.8171 (mmm) REVERT: B 340 GLU cc_start: 0.9100 (tp30) cc_final: 0.8607 (tm-30) REVERT: B 346 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8112 (tmm) REVERT: C 14 GLU cc_start: 0.9020 (mp0) cc_final: 0.8543 (mp0) REVERT: C 445 LYS cc_start: 0.9637 (tppp) cc_final: 0.9313 (tppp) outliers start: 19 outliers final: 13 residues processed: 70 average time/residue: 1.0767 time to fit residues: 83.9675 Evaluate side-chains 69 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 274 CYS 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 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 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 56 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.048771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.033305 restraints weight = 47455.634| |-----------------------------------------------------------------------------| r_work (start): 0.2430 rms_B_bonded: 4.49 r_work: 0.2264 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12305 Z= 0.141 Angle : 0.631 17.221 16709 Z= 0.299 Chirality : 0.043 0.245 1833 Planarity : 0.003 0.034 2144 Dihedral : 6.717 69.087 2083 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.40 % Allowed : 15.19 % Favored : 83.41 % 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 (0.22), residues: 1447 helix: 2.19 (0.27), residues: 378 sheet: 0.73 (0.30), residues: 287 loop : -1.06 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 343 HIS 0.005 0.001 HIS C 355 PHE 0.014 0.001 PHE A 439 TYR 0.008 0.001 TYR B 353 ARG 0.002 0.000 ARG B 452 Details of bonding type rmsd link_BETA2-3 : bond 0.00431 ( 3) link_BETA2-3 : angle 3.06226 ( 9) link_NAG-ASN : bond 0.00614 ( 11) link_NAG-ASN : angle 4.77503 ( 33) link_BETA1-4 : bond 0.00205 ( 5) link_BETA1-4 : angle 1.98861 ( 15) hydrogen bonds : bond 0.05309 ( 458) hydrogen bonds : angle 4.75052 ( 1383) SS BOND : bond 0.00161 ( 18) SS BOND : angle 1.17687 ( 36) covalent geometry : bond 0.00321 (12268) covalent geometry : angle 0.58554 (16616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6514.40 seconds wall clock time: 114 minutes 42.18 seconds (6882.18 seconds total)