Starting phenix.real_space_refine on Wed Sep 17 22:38:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhe_38348/09_2025/8xhe_38348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhe_38348/09_2025/8xhe_38348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xhe_38348/09_2025/8xhe_38348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhe_38348/09_2025/8xhe_38348.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xhe_38348/09_2025/8xhe_38348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhe_38348/09_2025/8xhe_38348.map" } resolution = 2.64 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= 0.001 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 75 5.16 5 C 7450 2.51 5 N 2011 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11912 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3878 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "A" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3873 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 19, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 3878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3878 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 19, 'TRANS': 469} Chain breaks: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "B" 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 Time building chain proxies: 2.79, per 1000 atoms: 0.23 Number of scatterers: 11912 At special positions: 0 Unit cell: (87.55, 86.7, 150.45, 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 75 16.00 O 2376 8.00 N 2011 7.00 C 7450 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.04 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 72 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " GAL D 1 " - " NAG D 2 " " GAL E 1 " - " NAG E 2 " " GAL F 1 " - " NAG F 2 " BETA1-4 " NAG D 2 " - " GAL D 3 " " NAG E 2 " - " GAL E 3 " " NAG F 2 " - " GAL F 3 " BETA2-6 " GAL D 3 " - " SIA D 4 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL E 3 " - " SIA E 4 " " GAL F 3 " - " SIA F 4 " NAG-ASN " NAG A 601 " - " ASN A 169 " " NAG A 602 " - " ASN A 484 " " NAG A 603 " - " ASN A 28 " " NAG B 601 " - " ASN B 169 " " NAG B 602 " - " ASN B 484 " " NAG B 603 " - " ASN B 28 " " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 28 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 568.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2686 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 33 sheets defined 27.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.557A pdb=" N LEU C 75 " --> pdb=" O CYS C 72 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 76' Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 367 through 388 removed outlier: 3.788A pdb=" N LYS C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 457 removed outlier: 3.852A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.803A pdb=" N ASN C 501 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.845A pdb=" N TRP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 368 through 387 Processing helix chain 'A' and resid 404 through 457 removed outlier: 3.841A pdb=" N ASP A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.841A pdb=" N SER A 496 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.957A pdb=" N ASP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARG B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.519A pdb=" N TRP B 127 " --> pdb=" O LYS B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 367 through 388 removed outlier: 3.659A pdb=" N THR B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 457 removed outlier: 3.875A pdb=" N GLU B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 488 through 501 removed outlier: 4.205A pdb=" N TYR B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 497 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 361 through 364 removed outlier: 3.666A pdb=" N GLY C 361 " --> pdb=" O ASN C 358 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 468 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.308A pdb=" N GLU C 19 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'C' and resid 46 through 49 removed outlier: 9.097A pdb=" N LEU C 46 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR C 280 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS C 48 " --> pdb=" O THR C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.813A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.696A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.696A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.990A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.515A pdb=" N ILE C 289 " --> pdb=" O CYS C 282 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.788A pdb=" N HIS A 356 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 363 " --> pdb=" O HIS A 356 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.938A pdb=" N GLU A 19 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AB7, first strand: chain 'A' and resid 46 through 49 removed outlier: 7.938A pdb=" N LEU A 46 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR A 280 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS A 48 " --> pdb=" O THR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.556A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 98 through 100 removed outlier: 6.606A pdb=" N SER A 99 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N TRP A 234 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS A 115 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG A 263 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 113 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 98 through 100 removed outlier: 6.606A pdb=" N SER A 99 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N TRP A 234 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.504A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'A' and resid 288 through 289 removed outlier: 4.189A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 460 through 462 Processing sheet with id=AC6, first strand: chain 'B' and resid 363 through 366 Processing sheet with id=AC7, first strand: chain 'B' and resid 19 through 21 removed outlier: 4.296A pdb=" N GLU B 19 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AC9, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AD1, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.091A pdb=" N LYS B 48 " --> pdb=" O THR B 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.763A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.364A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 98 through 100 removed outlier: 7.877A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.420A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 164 through 169 480 hydrogen bonds defined for protein. 1338 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: 2.07 Time building geometry restraints manager: 1.50 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: 3890 1.34 - 1.47: 2929 1.47 - 1.59: 5237 1.59 - 1.72: 0 1.72 - 1.84: 114 Bond restraints: 12170 Sorted by residual: bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C4 NAG E 2 " pdb=" O4 NAG E 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sigma weight residual 1.409 1.374 0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C4 NAG D 2 " pdb=" O4 NAG D 2 " ideal model delta sigma weight residual 1.409 1.375 0.034 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C6 GAL F 3 " pdb=" O6 GAL F 3 " ideal model delta sigma weight residual 1.407 1.374 0.033 2.00e-02 2.50e+03 2.76e+00 ... (remaining 12165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.75: 16456 6.75 - 13.51: 5 13.51 - 20.26: 5 20.26 - 27.01: 4 27.01 - 33.76: 1 Bond angle restraints: 16471 Sorted by residual: angle pdb=" C2 GAL F 1 " pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 107.49 141.25 -33.76 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C4 GAL F 1 " pdb=" C3 GAL F 1 " pdb=" O3 GAL F 1 " ideal model delta sigma weight residual 113.26 86.62 26.64 3.00e+00 1.11e-01 7.89e+01 angle pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sigma weight residual 107.29 132.32 -25.03 3.00e+00 1.11e-01 6.96e+01 angle pdb=" C4 GAL E 1 " pdb=" C3 GAL E 1 " pdb=" O3 GAL E 1 " ideal model delta sigma weight residual 113.26 89.33 23.93 3.00e+00 1.11e-01 6.36e+01 angle pdb=" C5 NAG D 2 " pdb=" C4 NAG D 2 " pdb=" O4 NAG D 2 " ideal model delta sigma weight residual 111.70 89.93 21.77 3.00e+00 1.11e-01 5.27e+01 ... (remaining 16466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.55: 6541 22.55 - 45.10: 831 45.10 - 67.64: 176 67.64 - 90.19: 37 90.19 - 112.74: 5 Dihedral angle restraints: 7590 sinusoidal: 3387 harmonic: 4203 Sorted by residual: dihedral pdb=" CB CYS C 282 " pdb=" SG CYS C 282 " pdb=" SG CYS C 306 " pdb=" CB CYS C 306 " ideal model delta sinusoidal sigma weight residual 93.00 36.17 56.83 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CB CYS A 9 " pdb=" SG CYS A 9 " pdb=" SG CYS A 467 " pdb=" CB CYS A 467 " ideal model delta sinusoidal sigma weight residual 93.00 50.77 42.23 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA CYS C 467 " pdb=" C CYS C 467 " pdb=" N PHE C 468 " pdb=" CA PHE C 468 " ideal model delta harmonic sigma weight residual 180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 7587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1817 0.127 - 0.254: 11 0.254 - 0.381: 0 0.381 - 0.507: 0 0.507 - 0.634: 2 Chirality restraints: 1830 Sorted by residual: chirality pdb=" C2 SIA E 4 " pdb=" O6 GAL E 3 " pdb=" C1 SIA E 4 " pdb=" O6 SIA E 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.67 0.17 2.00e-02 2.50e+03 7.42e+01 chirality pdb=" C2 SIA F 4 " pdb=" O6 GAL F 3 " pdb=" C1 SIA F 4 " pdb=" O6 SIA F 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.66 0.16 2.00e-02 2.50e+03 6.43e+01 chirality pdb=" C2 SIA D 4 " pdb=" O6 GAL D 3 " pdb=" C1 SIA D 4 " pdb=" O6 SIA D 4 " both_signs ideal model delta sigma weight residual False -2.50 -2.64 0.14 2.00e-02 2.50e+03 4.97e+01 ... (remaining 1827 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 306 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO B 307 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 306 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 307 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 293 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 294 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " 0.021 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 704 2.73 - 3.27: 10770 3.27 - 3.81: 19032 3.81 - 4.36: 23043 4.36 - 4.90: 40315 Nonbonded interactions: 93864 Sorted by model distance: nonbonded pdb=" OE2 GLU A 190 " pdb=" O9 SIA F 4 " model vdw 2.182 3.040 nonbonded pdb=" OG1 THR B 284 " pdb=" O GLY B 287 " model vdw 2.208 3.040 nonbonded pdb=" O6 SIA F 4 " pdb=" O8 SIA F 4 " model vdw 2.243 3.040 nonbonded pdb=" N GLU A 313 " pdb=" OE1 GLU A 313 " model vdw 2.259 3.120 nonbonded pdb=" O THR A 486 " pdb=" OG1 THR A 486 " model vdw 2.273 3.040 ... (remaining 93859 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 6 through 602) selection = (chain 'B' and (resid 6 through 327 or resid 336 through 602)) selection = (chain 'C' and (resid 6 through 327 or resid 336 through 602)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.490 Find NCS groups from input model: 0.320 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:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 0.062 12205 Z= 0.184 Angle : 0.882 33.763 16558 Z= 0.377 Chirality : 0.048 0.634 1830 Planarity : 0.004 0.043 2110 Dihedral : 19.715 112.738 4850 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.80 % Allowed : 33.64 % Favored : 61.56 % 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: -0.40 (0.22), residues: 1454 helix: 2.40 (0.27), residues: 367 sheet: 0.09 (0.35), residues: 252 loop : -1.74 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 126 TYR 0.012 0.001 TYR A 492 PHE 0.018 0.001 PHE A 339 TRP 0.006 0.001 TRP A 81 HIS 0.012 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00368 (12170) covalent geometry : angle 0.81641 (16471) SS BOND : bond 0.00405 ( 18) SS BOND : angle 1.17300 ( 36) hydrogen bonds : bond 0.18805 ( 448) hydrogen bonds : angle 6.95406 ( 1338) glycosidic custom : bond 0.06057 ( 3) glycosidic custom : angle 5.33463 ( 9) link_BETA1-3 : bond 0.04923 ( 3) link_BETA1-3 : angle 9.34155 ( 9) link_BETA1-4 : bond 0.03942 ( 3) link_BETA1-4 : angle 8.39704 ( 9) link_NAG-ASN : bond 0.00702 ( 8) link_NAG-ASN : angle 2.70142 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 329 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8256 (t) REVERT: C 458 ASP cc_start: 0.7202 (t0) cc_final: 0.6701 (t0) REVERT: C 473 LYS cc_start: 0.8556 (tptt) cc_final: 0.8324 (tppp) REVERT: A 142 SER cc_start: 0.8221 (p) cc_final: 0.7958 (t) REVERT: B 295 PHE cc_start: 0.7899 (m-80) cc_final: 0.7677 (m-80) outliers start: 62 outliers final: 53 residues processed: 382 average time/residue: 0.5888 time to fit residues: 242.4924 Evaluate side-chains 376 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 322 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 278 CYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 480 ASN A 210 ASN A 224 ASN A 472 HIS B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.111508 restraints weight = 16527.666| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.92 r_work: 0.3386 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12205 Z= 0.151 Angle : 0.576 8.665 16558 Z= 0.295 Chirality : 0.043 0.224 1830 Planarity : 0.004 0.041 2110 Dihedral : 10.221 106.756 2106 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.96 % Allowed : 29.85 % Favored : 64.19 % 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: -0.26 (0.22), residues: 1454 helix: 2.41 (0.27), residues: 382 sheet: 0.10 (0.33), residues: 272 loop : -1.68 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 126 TYR 0.013 0.001 TYR C 364 PHE 0.014 0.001 PHE C 440 TRP 0.007 0.001 TRP B 127 HIS 0.010 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00345 (12170) covalent geometry : angle 0.55986 (16471) SS BOND : bond 0.00431 ( 18) SS BOND : angle 1.22615 ( 36) hydrogen bonds : bond 0.05729 ( 448) hydrogen bonds : angle 5.10038 ( 1338) glycosidic custom : bond 0.00465 ( 3) glycosidic custom : angle 1.85291 ( 9) link_BETA1-3 : bond 0.00156 ( 3) link_BETA1-3 : angle 1.61757 ( 9) link_BETA1-4 : bond 0.00735 ( 3) link_BETA1-4 : angle 2.35755 ( 9) link_NAG-ASN : bond 0.00805 ( 8) link_NAG-ASN : angle 2.64648 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 336 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8549 (mtt-85) REVERT: C 458 ASP cc_start: 0.7565 (t0) cc_final: 0.7057 (t0) REVERT: C 473 LYS cc_start: 0.8674 (tptt) cc_final: 0.8380 (tppp) REVERT: C 497 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7717 (ttpt) REVERT: A 142 SER cc_start: 0.8228 (p) cc_final: 0.7958 (t) REVERT: A 435 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: A 488 ASP cc_start: 0.7821 (t0) cc_final: 0.7572 (t0) REVERT: A 491 LYS cc_start: 0.8432 (ttpp) cc_final: 0.8149 (ttpp) REVERT: B 151 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8140 (mmt) REVERT: B 187 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7583 (p0) REVERT: B 189 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8401 (p) REVERT: B 451 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7994 (ttmm) outliers start: 77 outliers final: 37 residues processed: 377 average time/residue: 0.6327 time to fit residues: 256.0849 Evaluate side-chains 369 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 326 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN A 210 ASN A 224 ASN A 299 HIS ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.125836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111689 restraints weight = 16576.525| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.93 r_work: 0.3396 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12205 Z= 0.147 Angle : 0.547 7.688 16558 Z= 0.284 Chirality : 0.042 0.206 1830 Planarity : 0.004 0.040 2110 Dihedral : 8.867 107.248 2049 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.57 % Allowed : 30.24 % Favored : 64.19 % 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: -0.17 (0.22), residues: 1454 helix: 2.51 (0.27), residues: 380 sheet: 0.16 (0.32), residues: 284 loop : -1.65 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 436 TYR 0.012 0.001 TYR B 354 PHE 0.022 0.001 PHE B 295 TRP 0.007 0.001 TRP B 65 HIS 0.009 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00339 (12170) covalent geometry : angle 0.53195 (16471) SS BOND : bond 0.00432 ( 18) SS BOND : angle 1.29244 ( 36) hydrogen bonds : bond 0.05576 ( 448) hydrogen bonds : angle 4.81602 ( 1338) glycosidic custom : bond 0.00458 ( 3) glycosidic custom : angle 1.12967 ( 9) link_BETA1-3 : bond 0.00265 ( 3) link_BETA1-3 : angle 1.24576 ( 9) link_BETA1-4 : bond 0.00063 ( 3) link_BETA1-4 : angle 2.37873 ( 9) link_NAG-ASN : bond 0.00718 ( 8) link_NAG-ASN : angle 2.59540 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 327 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8554 (mtt-85) REVERT: C 306 CYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7295 (m) REVERT: C 387 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7453 (pp20) REVERT: C 458 ASP cc_start: 0.7515 (t0) cc_final: 0.7009 (t0) REVERT: C 497 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7746 (ttpt) REVERT: A 137 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8065 (mmt) REVERT: A 142 SER cc_start: 0.8217 (p) cc_final: 0.7949 (t) REVERT: A 458 ASP cc_start: 0.8165 (t0) cc_final: 0.7708 (t0) REVERT: A 488 ASP cc_start: 0.7833 (t0) cc_final: 0.7562 (t0) REVERT: A 491 LYS cc_start: 0.8446 (ttpp) cc_final: 0.7971 (ttpp) REVERT: B 151 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8101 (mmt) REVERT: B 187 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7553 (p0) REVERT: B 451 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8012 (ttmm) REVERT: B 491 LYS cc_start: 0.8451 (tttm) cc_final: 0.8071 (tttm) outliers start: 72 outliers final: 37 residues processed: 362 average time/residue: 0.6618 time to fit residues: 257.1621 Evaluate side-chains 372 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 137 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 ASN A 16 ASN A 210 ASN A 224 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.125557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111483 restraints weight = 16653.750| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.93 r_work: 0.3394 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12205 Z= 0.155 Angle : 0.550 8.679 16558 Z= 0.286 Chirality : 0.042 0.202 1830 Planarity : 0.004 0.041 2110 Dihedral : 8.334 108.802 2038 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 6.19 % Allowed : 29.47 % Favored : 64.35 % 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: -0.20 (0.22), residues: 1454 helix: 2.52 (0.27), residues: 380 sheet: 0.11 (0.33), residues: 275 loop : -1.66 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 436 TYR 0.012 0.001 TYR B 354 PHE 0.014 0.001 PHE C 440 TRP 0.007 0.001 TRP B 65 HIS 0.009 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00362 (12170) covalent geometry : angle 0.53687 (16471) SS BOND : bond 0.00453 ( 18) SS BOND : angle 1.16618 ( 36) hydrogen bonds : bond 0.05494 ( 448) hydrogen bonds : angle 4.70610 ( 1338) glycosidic custom : bond 0.00269 ( 3) glycosidic custom : angle 0.91135 ( 9) link_BETA1-3 : bond 0.00186 ( 3) link_BETA1-3 : angle 0.89865 ( 9) link_BETA1-4 : bond 0.00112 ( 3) link_BETA1-4 : angle 2.06497 ( 9) link_NAG-ASN : bond 0.00715 ( 8) link_NAG-ASN : angle 2.57843 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 326 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8450 (mttp) REVERT: C 163 VAL cc_start: 0.8800 (t) cc_final: 0.8598 (p) REVERT: C 192 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8536 (mtt-85) REVERT: C 306 CYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7384 (m) REVERT: C 387 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7454 (pp20) REVERT: C 458 ASP cc_start: 0.7497 (t0) cc_final: 0.6991 (t0) REVERT: C 497 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7712 (ttpt) REVERT: A 137 MET cc_start: 0.8550 (mmm) cc_final: 0.8095 (mmt) REVERT: A 142 SER cc_start: 0.8221 (p) cc_final: 0.7955 (t) REVERT: A 458 ASP cc_start: 0.8166 (t0) cc_final: 0.7712 (t0) REVERT: A 488 ASP cc_start: 0.7812 (t0) cc_final: 0.7563 (t0) REVERT: A 491 LYS cc_start: 0.8456 (ttpp) cc_final: 0.7966 (ttpp) REVERT: B 27 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6414 (mpt90) REVERT: B 151 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8101 (mmt) REVERT: B 187 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7540 (p0) REVERT: B 362 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7714 (t) REVERT: B 451 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8002 (ttmm) outliers start: 80 outliers final: 42 residues processed: 375 average time/residue: 0.6335 time to fit residues: 255.6821 Evaluate side-chains 375 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 324 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 499 ASN A 16 ASN A 210 ASN A 224 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111021 restraints weight = 16585.725| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.93 r_work: 0.3384 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12205 Z= 0.167 Angle : 0.559 8.306 16558 Z= 0.291 Chirality : 0.043 0.196 1830 Planarity : 0.004 0.044 2110 Dihedral : 8.145 109.164 2037 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.65 % Allowed : 30.47 % Favored : 63.88 % 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: -0.20 (0.22), residues: 1454 helix: 2.50 (0.26), residues: 380 sheet: 0.08 (0.33), residues: 275 loop : -1.64 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 91 TYR 0.012 0.001 TYR B 354 PHE 0.023 0.001 PHE B 295 TRP 0.008 0.001 TRP B 65 HIS 0.011 0.001 HIS B 356 Details of bonding type rmsd covalent geometry : bond 0.00391 (12170) covalent geometry : angle 0.54591 (16471) SS BOND : bond 0.00453 ( 18) SS BOND : angle 1.32577 ( 36) hydrogen bonds : bond 0.05568 ( 448) hydrogen bonds : angle 4.65543 ( 1338) glycosidic custom : bond 0.00262 ( 3) glycosidic custom : angle 0.92308 ( 9) link_BETA1-3 : bond 0.00163 ( 3) link_BETA1-3 : angle 0.77990 ( 9) link_BETA1-4 : bond 0.00103 ( 3) link_BETA1-4 : angle 2.01241 ( 9) link_NAG-ASN : bond 0.00695 ( 8) link_NAG-ASN : angle 2.56718 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 327 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 192 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8523 (mtt-85) REVERT: C 387 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: C 458 ASP cc_start: 0.7507 (t0) cc_final: 0.7017 (t0) REVERT: C 497 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7710 (ttpt) REVERT: A 137 MET cc_start: 0.8559 (mmm) cc_final: 0.8214 (mmt) REVERT: A 142 SER cc_start: 0.8239 (p) cc_final: 0.7971 (t) REVERT: A 435 GLU cc_start: 0.7923 (tt0) cc_final: 0.7615 (tt0) REVERT: A 458 ASP cc_start: 0.8137 (t0) cc_final: 0.7684 (t0) REVERT: A 488 ASP cc_start: 0.7820 (t0) cc_final: 0.7584 (t0) REVERT: A 491 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8077 (ttpp) REVERT: B 151 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8170 (mmt) REVERT: B 187 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7555 (p0) REVERT: B 311 LYS cc_start: 0.7272 (tmmt) cc_final: 0.7018 (tmmt) REVERT: B 436 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6799 (mtp85) REVERT: B 451 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8012 (ttmm) REVERT: B 491 LYS cc_start: 0.8468 (tttm) cc_final: 0.8130 (tttm) outliers start: 73 outliers final: 41 residues processed: 366 average time/residue: 0.6322 time to fit residues: 248.6942 Evaluate side-chains 373 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 326 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 0.0970 chunk 101 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN A 50 ASN A 210 ASN A 224 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111502 restraints weight = 16640.912| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.93 r_work: 0.3378 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12205 Z= 0.143 Angle : 0.542 8.445 16558 Z= 0.282 Chirality : 0.042 0.199 1830 Planarity : 0.004 0.039 2110 Dihedral : 7.943 110.234 2035 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.10 % Allowed : 31.01 % Favored : 63.88 % 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: -0.13 (0.22), residues: 1454 helix: 2.57 (0.27), residues: 380 sheet: 0.16 (0.33), residues: 273 loop : -1.61 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.012 0.001 TYR B 12 PHE 0.013 0.001 PHE C 440 TRP 0.006 0.001 TRP B 65 HIS 0.010 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00331 (12170) covalent geometry : angle 0.52986 (16471) SS BOND : bond 0.00437 ( 18) SS BOND : angle 1.10162 ( 36) hydrogen bonds : bond 0.05367 ( 448) hydrogen bonds : angle 4.59547 ( 1338) glycosidic custom : bond 0.00222 ( 3) glycosidic custom : angle 0.80185 ( 9) link_BETA1-3 : bond 0.00207 ( 3) link_BETA1-3 : angle 0.69945 ( 9) link_BETA1-4 : bond 0.00050 ( 3) link_BETA1-4 : angle 1.87989 ( 9) link_NAG-ASN : bond 0.00691 ( 8) link_NAG-ASN : angle 2.50407 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 327 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8438 (mttp) REVERT: C 163 VAL cc_start: 0.8790 (t) cc_final: 0.8583 (p) REVERT: C 458 ASP cc_start: 0.7461 (t0) cc_final: 0.6976 (t0) REVERT: C 497 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7681 (ttpt) REVERT: A 137 MET cc_start: 0.8540 (mmm) cc_final: 0.8229 (mmt) REVERT: A 142 SER cc_start: 0.8237 (p) cc_final: 0.7960 (t) REVERT: A 389 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7324 (mmt) REVERT: A 435 GLU cc_start: 0.7889 (tt0) cc_final: 0.7425 (tt0) REVERT: A 458 ASP cc_start: 0.8215 (t0) cc_final: 0.7774 (t0) REVERT: A 488 ASP cc_start: 0.7811 (t0) cc_final: 0.7563 (t0) REVERT: A 491 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8220 (ttpp) REVERT: A 492 TYR cc_start: 0.6852 (m-80) cc_final: 0.6358 (m-80) REVERT: B 27 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6426 (mpt90) REVERT: B 151 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8111 (mmt) REVERT: B 187 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7531 (p0) REVERT: B 311 LYS cc_start: 0.7281 (tmmt) cc_final: 0.7030 (tmmt) REVERT: B 436 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6666 (mtp85) REVERT: B 451 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8013 (ttmm) REVERT: B 491 LYS cc_start: 0.8454 (tttm) cc_final: 0.8089 (tttm) outliers start: 66 outliers final: 37 residues processed: 362 average time/residue: 0.6658 time to fit residues: 258.3550 Evaluate side-chains 366 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 21 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 484 ASN A 224 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN B 480 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111270 restraints weight = 16586.010| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.93 r_work: 0.3386 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12205 Z= 0.154 Angle : 0.552 8.381 16558 Z= 0.288 Chirality : 0.042 0.198 1830 Planarity : 0.004 0.039 2110 Dihedral : 7.769 110.677 2032 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.87 % Allowed : 32.25 % Favored : 62.88 % 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: -0.13 (0.22), residues: 1454 helix: 2.58 (0.26), residues: 380 sheet: 0.15 (0.33), residues: 273 loop : -1.61 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 457 TYR 0.012 0.001 TYR B 12 PHE 0.023 0.001 PHE B 295 TRP 0.007 0.001 TRP B 65 HIS 0.009 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00361 (12170) covalent geometry : angle 0.54039 (16471) SS BOND : bond 0.00434 ( 18) SS BOND : angle 1.14084 ( 36) hydrogen bonds : bond 0.05410 ( 448) hydrogen bonds : angle 4.56909 ( 1338) glycosidic custom : bond 0.00222 ( 3) glycosidic custom : angle 0.83300 ( 9) link_BETA1-3 : bond 0.00188 ( 3) link_BETA1-3 : angle 0.66987 ( 9) link_BETA1-4 : bond 0.00045 ( 3) link_BETA1-4 : angle 1.86073 ( 9) link_NAG-ASN : bond 0.00675 ( 8) link_NAG-ASN : angle 2.49450 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 325 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8448 (mttp) REVERT: C 387 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7490 (pp20) REVERT: C 458 ASP cc_start: 0.7503 (t0) cc_final: 0.7057 (t0) REVERT: C 497 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7703 (ttpt) REVERT: A 137 MET cc_start: 0.8551 (mmm) cc_final: 0.8255 (mmt) REVERT: A 142 SER cc_start: 0.8241 (p) cc_final: 0.7968 (t) REVERT: A 389 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7282 (mmt) REVERT: A 435 GLU cc_start: 0.7891 (tt0) cc_final: 0.7396 (tt0) REVERT: A 458 ASP cc_start: 0.8181 (t0) cc_final: 0.7787 (t0) REVERT: A 488 ASP cc_start: 0.7839 (t0) cc_final: 0.7576 (t0) REVERT: A 491 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8212 (ttpp) REVERT: A 492 TYR cc_start: 0.6841 (m-80) cc_final: 0.6346 (m-80) REVERT: B 27 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.6390 (mpt90) REVERT: B 151 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8103 (mmt) REVERT: B 187 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7522 (p0) REVERT: B 311 LYS cc_start: 0.7283 (tmmt) cc_final: 0.7035 (tmmt) REVERT: B 436 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6690 (mtp85) REVERT: B 451 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8010 (ttmm) REVERT: B 491 LYS cc_start: 0.8480 (tttm) cc_final: 0.8129 (tttm) outliers start: 63 outliers final: 41 residues processed: 360 average time/residue: 0.6384 time to fit residues: 246.7478 Evaluate side-chains 373 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 356 HIS A 16 ASN A 224 ASN ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.111381 restraints weight = 16524.112| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.93 r_work: 0.3389 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12205 Z= 0.147 Angle : 0.551 8.180 16558 Z= 0.288 Chirality : 0.042 0.199 1830 Planarity : 0.004 0.038 2110 Dihedral : 7.596 111.502 2030 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.10 % Allowed : 32.48 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.09 (0.22), residues: 1454 helix: 2.61 (0.26), residues: 380 sheet: 0.19 (0.33), residues: 273 loop : -1.59 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 212 TYR 0.013 0.001 TYR B 489 PHE 0.021 0.001 PHE A 339 TRP 0.006 0.001 TRP B 422 HIS 0.010 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00340 (12170) covalent geometry : angle 0.53924 (16471) SS BOND : bond 0.00423 ( 18) SS BOND : angle 1.11409 ( 36) hydrogen bonds : bond 0.05338 ( 448) hydrogen bonds : angle 4.54163 ( 1338) glycosidic custom : bond 0.00233 ( 3) glycosidic custom : angle 0.80577 ( 9) link_BETA1-3 : bond 0.00204 ( 3) link_BETA1-3 : angle 0.67486 ( 9) link_BETA1-4 : bond 0.00033 ( 3) link_BETA1-4 : angle 1.81888 ( 9) link_NAG-ASN : bond 0.00677 ( 8) link_NAG-ASN : angle 2.46105 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 319 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8444 (mttp) REVERT: C 280 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8350 (t) REVERT: C 387 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7497 (pp20) REVERT: C 458 ASP cc_start: 0.7533 (t0) cc_final: 0.7057 (t0) REVERT: A 137 MET cc_start: 0.8571 (mmm) cc_final: 0.8227 (mmt) REVERT: A 142 SER cc_start: 0.8234 (p) cc_final: 0.7960 (t) REVERT: A 389 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7292 (mmt) REVERT: A 435 GLU cc_start: 0.7880 (tt0) cc_final: 0.7324 (tt0) REVERT: A 458 ASP cc_start: 0.8196 (t0) cc_final: 0.7800 (t0) REVERT: A 488 ASP cc_start: 0.7846 (t0) cc_final: 0.7586 (t0) REVERT: A 491 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8210 (ttpp) REVERT: A 492 TYR cc_start: 0.6841 (m-80) cc_final: 0.6336 (m-80) REVERT: B 27 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6384 (mpt90) REVERT: B 151 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8116 (mmt) REVERT: B 187 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7533 (p0) REVERT: B 311 LYS cc_start: 0.7267 (tmmt) cc_final: 0.7047 (tmmt) REVERT: B 387 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7834 (mm-30) REVERT: B 436 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6664 (mtp85) REVERT: B 451 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8001 (ttmm) REVERT: B 479 MET cc_start: 0.7468 (mmt) cc_final: 0.7062 (mmt) REVERT: B 491 LYS cc_start: 0.8433 (tttm) cc_final: 0.8090 (tttm) outliers start: 66 outliers final: 42 residues processed: 360 average time/residue: 0.6549 time to fit residues: 252.7992 Evaluate side-chains 366 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 356 HIS A 224 ASN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.122775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108778 restraints weight = 16417.712| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.93 r_work: 0.3353 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 12205 Z= 0.296 Angle : 0.666 9.268 16558 Z= 0.347 Chirality : 0.048 0.174 1830 Planarity : 0.004 0.039 2110 Dihedral : 7.781 109.646 2030 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.56 % Allowed : 32.71 % Favored : 62.72 % 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: -0.42 (0.21), residues: 1454 helix: 2.25 (0.26), residues: 380 sheet: 0.00 (0.32), residues: 276 loop : -1.75 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 457 TYR 0.028 0.002 TYR C 489 PHE 0.027 0.002 PHE B 295 TRP 0.012 0.002 TRP B 65 HIS 0.011 0.002 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00711 (12170) covalent geometry : angle 0.65388 (16471) SS BOND : bond 0.00555 ( 18) SS BOND : angle 1.41257 ( 36) hydrogen bonds : bond 0.06389 ( 448) hydrogen bonds : angle 4.79045 ( 1338) glycosidic custom : bond 0.00680 ( 3) glycosidic custom : angle 1.24078 ( 9) link_BETA1-3 : bond 0.00109 ( 3) link_BETA1-3 : angle 0.87221 ( 9) link_BETA1-4 : bond 0.00238 ( 3) link_BETA1-4 : angle 2.16513 ( 9) link_NAG-ASN : bond 0.00700 ( 8) link_NAG-ASN : angle 2.72275 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 326 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7554 (pp20) REVERT: C 458 ASP cc_start: 0.7576 (t0) cc_final: 0.7120 (t0) REVERT: C 497 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7712 (ttpt) REVERT: A 137 MET cc_start: 0.8613 (mmm) cc_final: 0.8252 (mmt) REVERT: A 142 SER cc_start: 0.8285 (p) cc_final: 0.8008 (t) REVERT: A 278 CYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6528 (p) REVERT: A 389 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7330 (mmt) REVERT: A 435 GLU cc_start: 0.7838 (tt0) cc_final: 0.7224 (tt0) REVERT: A 458 ASP cc_start: 0.8151 (t0) cc_final: 0.7742 (t0) REVERT: A 491 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8166 (ttpp) REVERT: B 27 ARG cc_start: 0.6870 (OUTLIER) cc_final: 0.6603 (mpt90) REVERT: B 151 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8104 (mmt) REVERT: B 187 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7534 (p0) REVERT: B 311 LYS cc_start: 0.7358 (tmmt) cc_final: 0.7096 (tmmt) REVERT: B 436 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6710 (mtp85) REVERT: B 451 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8012 (ttmm) REVERT: B 491 LYS cc_start: 0.8524 (tttm) cc_final: 0.8182 (tttm) outliers start: 59 outliers final: 37 residues processed: 354 average time/residue: 0.6615 time to fit residues: 251.4208 Evaluate side-chains 367 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 321 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 402 ASN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 388 LYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 356 HIS C 447 ASN C 459 ASN A 16 ASN A 50 ASN A 224 ASN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.124940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110883 restraints weight = 16560.318| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.92 r_work: 0.3378 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12205 Z= 0.155 Angle : 0.583 8.859 16558 Z= 0.303 Chirality : 0.043 0.188 1830 Planarity : 0.004 0.039 2110 Dihedral : 7.476 111.764 2028 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.33 % Allowed : 34.26 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.19 (0.22), residues: 1454 helix: 2.57 (0.26), residues: 378 sheet: 0.13 (0.32), residues: 274 loop : -1.66 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 212 TYR 0.027 0.002 TYR C 489 PHE 0.026 0.001 PHE B 295 TRP 0.007 0.001 TRP B 65 HIS 0.011 0.001 HIS C 356 Details of bonding type rmsd covalent geometry : bond 0.00361 (12170) covalent geometry : angle 0.57132 (16471) SS BOND : bond 0.00441 ( 18) SS BOND : angle 1.21092 ( 36) hydrogen bonds : bond 0.05559 ( 448) hydrogen bonds : angle 4.64770 ( 1338) glycosidic custom : bond 0.00275 ( 3) glycosidic custom : angle 0.87997 ( 9) link_BETA1-3 : bond 0.00196 ( 3) link_BETA1-3 : angle 0.68746 ( 9) link_BETA1-4 : bond 0.00032 ( 3) link_BETA1-4 : angle 1.87754 ( 9) link_NAG-ASN : bond 0.00712 ( 8) link_NAG-ASN : angle 2.49875 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2908 Ramachandran restraints generated. 1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 280 THR cc_start: 0.8579 (p) cc_final: 0.8369 (t) REVERT: C 387 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7533 (pp20) REVERT: C 452 VAL cc_start: 0.8460 (t) cc_final: 0.8234 (p) REVERT: C 458 ASP cc_start: 0.7531 (t0) cc_final: 0.7069 (t0) REVERT: A 26 GLU cc_start: 0.7614 (tp30) cc_final: 0.7404 (tp30) REVERT: A 137 MET cc_start: 0.8580 (mmm) cc_final: 0.8242 (mmt) REVERT: A 142 SER cc_start: 0.8279 (p) cc_final: 0.7996 (t) REVERT: A 435 GLU cc_start: 0.7827 (tt0) cc_final: 0.7097 (tt0) REVERT: A 458 ASP cc_start: 0.8146 (t0) cc_final: 0.7751 (t0) REVERT: A 491 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8140 (ttpp) REVERT: B 151 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8142 (mmt) REVERT: B 187 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7501 (p0) REVERT: B 311 LYS cc_start: 0.7313 (tmmt) cc_final: 0.7064 (tmmt) REVERT: B 436 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6626 (mtp85) REVERT: B 451 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8006 (ttmm) REVERT: B 491 LYS cc_start: 0.8456 (tttm) cc_final: 0.8088 (tttm) REVERT: B 497 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8003 (tmtm) outliers start: 43 outliers final: 29 residues processed: 339 average time/residue: 0.6527 time to fit residues: 237.1870 Evaluate side-chains 352 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 157 LYS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 30 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 356 HIS C 459 ASN A 50 ASN A 224 ASN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 296 HIS ** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109372 restraints weight = 16665.013| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.92 r_work: 0.3341 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 12205 Z= 0.284 Angle : 0.654 8.562 16558 Z= 0.342 Chirality : 0.047 0.171 1830 Planarity : 0.004 0.040 2110 Dihedral : 7.603 110.568 2028 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.48 % Allowed : 33.80 % Favored : 62.72 % 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: -0.38 (0.21), residues: 1454 helix: 2.31 (0.26), residues: 380 sheet: 0.10 (0.32), residues: 273 loop : -1.77 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 212 TYR 0.029 0.002 TYR C 489 PHE 0.019 0.002 PHE A 339 TRP 0.012 0.002 TRP B 65 HIS 0.011 0.002 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00680 (12170) covalent geometry : angle 0.64141 (16471) SS BOND : bond 0.00591 ( 18) SS BOND : angle 1.46194 ( 36) hydrogen bonds : bond 0.06281 ( 448) hydrogen bonds : angle 4.77331 ( 1338) glycosidic custom : bond 0.00590 ( 3) glycosidic custom : angle 1.15340 ( 9) link_BETA1-3 : bond 0.00100 ( 3) link_BETA1-3 : angle 0.83246 ( 9) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 2.13714 ( 9) link_NAG-ASN : bond 0.00713 ( 8) link_NAG-ASN : angle 2.71132 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5368.32 seconds wall clock time: 92 minutes 1.96 seconds (5521.96 seconds total)