Starting phenix.real_space_refine on Sat Jan 18 06:59:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhe_38348/01_2025/8xhe_38348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhe_38348/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhe_38348/01_2025/8xhe_38348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhe_38348/01_2025/8xhe_38348.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhe_38348/01_2025/8xhe_38348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhe_38348/01_2025/8xhe_38348.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 7.51, per 1000 atoms: 0.63 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: 3.55 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.66 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: 4.11 Time building geometry restraints manager: 3.93 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 501 or resid 601 through 602)) selection = (chain 'B' and (resid 6 through 327 or resid 336 through 501 or resid 601 throug \ h 602)) selection = (chain 'C' and (resid 6 through 327 or resid 336 through 501 or resid 601 throug \ h 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.090 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.670 ------------------------------------------------------------------------------- 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 0.036 12170 Z= 0.242 Angle : 0.816 33.763 16471 Z= 0.360 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 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 TRP 0.006 0.001 TRP A 81 HIS 0.012 0.001 HIS B 356 PHE 0.018 0.001 PHE A 339 TYR 0.012 0.001 TYR A 492 ARG 0.007 0.001 ARG B 126 *********************** 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 : 1.368 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: 1.2895 time to fit residues: 530.8981 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 : 1.378 ------------------------------------------------------------------------------- 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 121 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.124736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110516 restraints weight = 16358.309| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.93 r_work: 0.3388 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12170 Z= 0.265 Angle : 0.571 8.363 16471 Z= 0.297 Chirality : 0.043 0.219 1830 Planarity : 0.004 0.043 2110 Dihedral : 10.238 106.563 2106 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1454 helix: 2.37 (0.27), residues: 382 sheet: 0.14 (0.32), residues: 280 loop : -1.69 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 127 HIS 0.011 0.002 HIS B 356 PHE 0.015 0.001 PHE C 440 TYR 0.013 0.002 TYR C 364 ARG 0.007 0.001 ARG B 126 *********************** 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 414 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 337 time to evaluate : 1.421 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: 0.8767 (ttm-80) cc_final: 0.8547 (mtt-85) REVERT: C 458 ASP cc_start: 0.7573 (t0) cc_final: 0.7062 (t0) REVERT: C 473 LYS cc_start: 0.8679 (tptt) cc_final: 0.8387 (tppp) REVERT: C 497 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7743 (ttpt) REVERT: A 142 SER cc_start: 0.8228 (p) cc_final: 0.7964 (t) REVERT: A 488 ASP cc_start: 0.7841 (t0) cc_final: 0.7594 (t0) REVERT: A 491 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8152 (ttpp) REVERT: B 151 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8189 (mmt) REVERT: B 451 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7998 (ttmm) outliers start: 77 outliers final: 39 residues processed: 378 average time/residue: 1.3960 time to fit residues: 567.4407 Evaluate side-chains 370 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 328 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 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 116 PHE Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 151 MET 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 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 32 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 78 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- 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 50 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.110529 restraints weight = 16601.241| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.94 r_work: 0.3381 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12170 Z= 0.295 Angle : 0.556 7.867 16471 Z= 0.294 Chirality : 0.043 0.199 1830 Planarity : 0.004 0.043 2110 Dihedral : 8.967 106.539 2050 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.80 % Allowed : 29.70 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1454 helix: 2.43 (0.27), residues: 380 sheet: 0.01 (0.32), residues: 276 loop : -1.70 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 65 HIS 0.009 0.002 HIS A 472 PHE 0.021 0.002 PHE B 295 TYR 0.014 0.002 TYR C 424 ARG 0.003 0.000 ARG C 74 *********************** 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 404 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 329 time to evaluate : 1.459 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: 0.8766 (ttm-80) cc_final: 0.8555 (mtt-85) REVERT: C 306 CYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7260 (m) REVERT: C 387 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7464 (pp20) REVERT: C 436 ARG cc_start: 0.7760 (mpp80) cc_final: 0.7513 (mpp80) REVERT: C 458 ASP cc_start: 0.7552 (t0) cc_final: 0.7039 (t0) REVERT: C 497 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7756 (ttpt) REVERT: A 137 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8083 (mmt) REVERT: A 142 SER cc_start: 0.8226 (p) cc_final: 0.7958 (t) REVERT: A 458 ASP cc_start: 0.8084 (t0) cc_final: 0.7624 (t0) REVERT: A 488 ASP cc_start: 0.7853 (t0) cc_final: 0.7591 (t0) REVERT: A 491 LYS cc_start: 0.8465 (ttpp) cc_final: 0.7985 (ttpp) REVERT: B 27 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6399 (mpt90) REVERT: B 151 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8170 (mmt) REVERT: B 362 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7725 (t) REVERT: B 451 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8001 (ttmm) REVERT: B 457 ARG cc_start: 0.7289 (mtm180) cc_final: 0.7065 (mtm180) REVERT: B 491 LYS cc_start: 0.8473 (tttm) cc_final: 0.8090 (tttm) outliers start: 75 outliers final: 37 residues processed: 370 average time/residue: 1.4517 time to fit residues: 576.6912 Evaluate side-chains 372 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 327 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 310 VAL 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 236 LEU 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 362 SER 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 497 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 135 optimal weight: 0.0060 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 ASN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 GLN ** 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 ** B 380 ASN ** 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 = 0.3720 r_free = 0.3720 target = 0.126677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.112522 restraints weight = 16491.557| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.94 r_work: 0.3407 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12170 Z= 0.158 Angle : 0.510 8.461 16471 Z= 0.268 Chirality : 0.041 0.211 1830 Planarity : 0.004 0.041 2110 Dihedral : 8.266 109.874 2040 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.18 % Allowed : 30.24 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1454 helix: 2.61 (0.27), residues: 380 sheet: 0.15 (0.33), residues: 275 loop : -1.61 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 422 HIS 0.010 0.001 HIS B 356 PHE 0.010 0.001 PHE C 440 TYR 0.014 0.001 TYR B 354 ARG 0.003 0.000 ARG C 212 *********************** 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 393 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 326 time to evaluate : 1.403 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: 0.8692 (OUTLIER) cc_final: 0.8446 (mttp) REVERT: C 192 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8543 (mtt-85) REVERT: C 306 CYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7416 (m) REVERT: C 432 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7159 (mpp) REVERT: C 436 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7432 (mpp80) REVERT: C 458 ASP cc_start: 0.7464 (t0) cc_final: 0.6960 (t0) REVERT: C 497 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7712 (ttpt) REVERT: A 137 MET cc_start: 0.8548 (mmm) cc_final: 0.8103 (mmt) REVERT: A 142 SER cc_start: 0.8225 (p) cc_final: 0.7952 (t) REVERT: A 458 ASP cc_start: 0.8171 (t0) cc_final: 0.7729 (t0) REVERT: A 488 ASP cc_start: 0.7790 (t0) cc_final: 0.7563 (t0) REVERT: A 491 LYS cc_start: 0.8442 (ttpp) cc_final: 0.8241 (tmmm) REVERT: B 27 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6390 (mpt90) REVERT: B 187 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7472 (p0) REVERT: B 451 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8001 (ttmm) REVERT: B 479 MET cc_start: 0.7427 (mmt) cc_final: 0.6993 (mmt) REVERT: B 491 LYS cc_start: 0.8457 (tttm) cc_final: 0.8221 (tttm) outliers start: 67 outliers final: 35 residues processed: 364 average time/residue: 1.3745 time to fit residues: 537.3590 Evaluate side-chains 361 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 40 LYS 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 391 THR Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 436 ARG 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 128 THR Chi-restraints excluded: chain A residue 139 CYS 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 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 187 ASP Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 321 LEU 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 497 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 ASN ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.126046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111944 restraints weight = 16498.571| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.92 r_work: 0.3393 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12170 Z= 0.225 Angle : 0.542 12.527 16471 Z= 0.281 Chirality : 0.042 0.206 1830 Planarity : 0.004 0.041 2110 Dihedral : 8.042 109.716 2033 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.80 % Allowed : 31.48 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1454 helix: 2.53 (0.27), residues: 380 sheet: 0.16 (0.33), residues: 275 loop : -1.60 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 65 HIS 0.010 0.001 HIS B 356 PHE 0.022 0.001 PHE B 295 TYR 0.011 0.001 TYR B 12 ARG 0.003 0.000 ARG B 74 *********************** 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 380 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 318 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8445 (mttp) REVERT: C 192 ARG cc_start: 0.8769 (ttm-80) cc_final: 0.8537 (mtt-85) REVERT: C 387 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7455 (pp20) REVERT: C 432 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7167 (mpp) REVERT: C 436 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7443 (mpp80) REVERT: C 458 ASP cc_start: 0.7506 (t0) cc_final: 0.7015 (t0) REVERT: C 497 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7712 (ttpt) REVERT: A 137 MET cc_start: 0.8575 (mmm) cc_final: 0.8251 (mmt) REVERT: A 142 SER cc_start: 0.8227 (p) cc_final: 0.7955 (t) REVERT: A 458 ASP cc_start: 0.8171 (t0) cc_final: 0.7735 (t0) REVERT: A 488 ASP cc_start: 0.7794 (t0) cc_final: 0.7561 (t0) REVERT: A 491 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8208 (tmmm) REVERT: B 187 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7480 (p0) REVERT: B 362 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7714 (t) REVERT: B 451 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8007 (ttmm) outliers start: 62 outliers final: 34 residues processed: 352 average time/residue: 1.4334 time to fit residues: 542.7621 Evaluate side-chains 361 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 319 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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 396 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 436 ARG 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 128 THR Chi-restraints excluded: chain A residue 139 CYS 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 B residue 20 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 71 GLU 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 187 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 ASN ** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3687 r_free = 0.3687 target = 0.124052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109888 restraints weight = 16508.781| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.93 r_work: 0.3369 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12170 Z= 0.365 Angle : 0.599 11.701 16471 Z= 0.314 Chirality : 0.045 0.186 1830 Planarity : 0.004 0.038 2110 Dihedral : 7.984 108.886 2029 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.03 % Allowed : 31.25 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.22), residues: 1454 helix: 2.36 (0.26), residues: 380 sheet: 0.08 (0.32), residues: 274 loop : -1.67 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 65 HIS 0.011 0.002 HIS B 356 PHE 0.013 0.002 PHE C 440 TYR 0.015 0.002 TYR C 424 ARG 0.003 0.000 ARG C 212 *********************** 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 389 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 324 time to evaluate : 1.360 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: 0.7762 (OUTLIER) cc_final: 0.7513 (pp20) REVERT: C 432 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7154 (mpp) REVERT: C 436 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7449 (mpp80) REVERT: C 458 ASP cc_start: 0.7501 (t0) cc_final: 0.7010 (t0) REVERT: C 497 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7699 (ttpt) REVERT: A 137 MET cc_start: 0.8584 (mmm) cc_final: 0.8277 (mmt) REVERT: A 142 SER cc_start: 0.8256 (p) cc_final: 0.7977 (t) REVERT: A 458 ASP cc_start: 0.8100 (t0) cc_final: 0.7657 (t0) REVERT: A 488 ASP cc_start: 0.7847 (t0) cc_final: 0.7592 (t0) REVERT: A 491 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8214 (ttpp) REVERT: A 492 TYR cc_start: 0.6838 (m-80) cc_final: 0.6349 (m-80) REVERT: B 27 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6441 (mpt90) REVERT: B 151 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8151 (mmt) REVERT: B 187 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7494 (p0) REVERT: B 276 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: B 311 LYS cc_start: 0.7256 (tmmt) cc_final: 0.6986 (tmmt) REVERT: B 362 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7716 (t) REVERT: B 451 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8005 (ttmm) REVERT: B 491 LYS cc_start: 0.8513 (tttm) cc_final: 0.8195 (tttm) outliers start: 65 outliers final: 36 residues processed: 358 average time/residue: 1.3800 time to fit residues: 530.5658 Evaluate side-chains 368 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 402 ASN Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 436 ARG 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 128 THR 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 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 40 LYS Chi-restraints excluded: chain B residue 78 VAL 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 276 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 69 optimal weight: 0.0470 chunk 119 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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** 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 480 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109283 restraints weight = 16610.706| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.97 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: 0.8054 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12170 Z= 0.199 Angle : 0.545 9.714 16471 Z= 0.285 Chirality : 0.042 0.202 1830 Planarity : 0.004 0.039 2110 Dihedral : 7.665 111.185 2027 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.10 % Allowed : 33.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1454 helix: 2.62 (0.27), residues: 378 sheet: 0.20 (0.33), residues: 273 loop : -1.61 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 422 HIS 0.012 0.001 HIS B 356 PHE 0.023 0.001 PHE B 295 TYR 0.014 0.001 TYR B 489 ARG 0.008 0.000 ARG C 74 *********************** 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 370 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 317 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 276 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: C 280 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8344 (t) REVERT: C 387 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7492 (pp20) REVERT: C 432 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7219 (mpp) REVERT: C 436 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7463 (mpp80) REVERT: C 458 ASP cc_start: 0.7445 (t0) cc_final: 0.6972 (t0) REVERT: C 497 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7700 (ttpt) REVERT: A 137 MET cc_start: 0.8550 (mmm) cc_final: 0.8204 (mmt) REVERT: A 142 SER cc_start: 0.8236 (p) cc_final: 0.7955 (t) REVERT: A 389 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7352 (mmt) REVERT: A 458 ASP cc_start: 0.8149 (t0) cc_final: 0.7732 (t0) REVERT: A 488 ASP cc_start: 0.7824 (t0) cc_final: 0.7576 (t0) REVERT: A 491 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8218 (ttpp) REVERT: A 492 TYR cc_start: 0.6818 (m-80) cc_final: 0.6321 (m-80) REVERT: B 27 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6402 (mpt90) REVERT: B 187 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7424 (p0) REVERT: B 451 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7987 (ttmm) REVERT: B 479 MET cc_start: 0.7453 (mmt) cc_final: 0.7044 (mmt) REVERT: B 491 LYS cc_start: 0.8406 (tttm) cc_final: 0.8056 (tttm) outliers start: 53 outliers final: 28 residues processed: 346 average time/residue: 1.4111 time to fit residues: 523.9628 Evaluate side-chains 351 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 313 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 230 MET Chi-restraints excluded: chain C residue 276 GLU 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 432 MET Chi-restraints excluded: chain C residue 436 ARG 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 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 389 MET 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 187 ASP 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 456 LEU 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 30 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 484 ASN A 16 ASN A 50 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.124978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110890 restraints weight = 16587.450| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.94 r_work: 0.3383 rms_B_bonded: 2.30 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: 0.8069 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12170 Z= 0.264 Angle : 0.567 10.028 16471 Z= 0.297 Chirality : 0.043 0.198 1830 Planarity : 0.004 0.041 2110 Dihedral : 7.520 111.074 2024 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.41 % Allowed : 32.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1454 helix: 2.52 (0.26), residues: 380 sheet: 0.19 (0.33), residues: 273 loop : -1.62 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 65 HIS 0.012 0.002 HIS B 356 PHE 0.021 0.002 PHE A 339 TYR 0.013 0.001 TYR B 12 ARG 0.007 0.000 ARG C 74 *********************** 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 380 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 323 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 276 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: C 387 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7536 (pp20) REVERT: C 432 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7184 (mpp) REVERT: C 436 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7442 (mpp80) REVERT: C 457 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6898 (ttm170) REVERT: C 458 ASP cc_start: 0.7593 (t0) cc_final: 0.7179 (t0) REVERT: C 497 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7691 (ttpt) REVERT: A 137 MET cc_start: 0.8586 (mmm) cc_final: 0.8250 (mmt) REVERT: A 142 SER cc_start: 0.8225 (p) cc_final: 0.7943 (t) REVERT: A 389 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7361 (mmt) REVERT: A 458 ASP cc_start: 0.8122 (t0) cc_final: 0.7734 (t0) REVERT: A 488 ASP cc_start: 0.7846 (t0) cc_final: 0.7605 (t0) REVERT: A 491 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8211 (ttpp) REVERT: A 492 TYR cc_start: 0.6838 (m-80) cc_final: 0.6323 (m-80) REVERT: B 27 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6479 (mpt90) REVERT: B 151 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8162 (mmt) REVERT: B 187 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7485 (p0) REVERT: B 451 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8005 (ttmm) REVERT: B 463 LEU cc_start: 0.8805 (mp) cc_final: 0.8601 (mt) REVERT: B 479 MET cc_start: 0.7489 (mmt) cc_final: 0.7055 (mmt) REVERT: B 491 LYS cc_start: 0.8453 (tttm) cc_final: 0.8095 (tttm) outliers start: 57 outliers final: 35 residues processed: 352 average time/residue: 1.3701 time to fit residues: 518.0949 Evaluate side-chains 363 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 ILE 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 276 GLU 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 432 MET Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 457 ARG 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 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 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 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 456 LEU 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 138 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 50 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 480 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.124740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110272 restraints weight = 16481.492| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.98 r_work: 0.3365 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12170 Z= 0.352 Angle : 0.607 10.073 16471 Z= 0.319 Chirality : 0.045 0.188 1830 Planarity : 0.004 0.043 2110 Dihedral : 7.515 110.937 2024 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.33 % Allowed : 33.49 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1454 helix: 2.40 (0.26), residues: 380 sheet: 0.11 (0.32), residues: 274 loop : -1.67 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 65 HIS 0.011 0.002 HIS C 356 PHE 0.026 0.002 PHE B 295 TYR 0.015 0.002 TYR C 424 ARG 0.007 0.001 ARG C 74 *********************** 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 381 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 325 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8256 (t) REVERT: C 276 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: C 387 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: C 432 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7172 (mpp) REVERT: C 436 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7453 (mpp80) REVERT: C 457 ARG cc_start: 0.7180 (mtm180) cc_final: 0.6899 (mtm180) REVERT: C 458 ASP cc_start: 0.7575 (t0) cc_final: 0.7135 (t0) REVERT: A 80 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6955 (tm-30) REVERT: A 137 MET cc_start: 0.8601 (mmm) cc_final: 0.8241 (mmt) REVERT: A 142 SER cc_start: 0.8268 (p) cc_final: 0.7981 (t) REVERT: A 389 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7388 (mmt) REVERT: A 458 ASP cc_start: 0.8124 (t0) cc_final: 0.7732 (t0) REVERT: A 491 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8151 (ttpp) REVERT: B 27 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6484 (mpt90) REVERT: B 151 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8163 (mmt) REVERT: B 187 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7462 (p0) REVERT: B 451 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8016 (ttmm) REVERT: B 491 LYS cc_start: 0.8481 (tttm) cc_final: 0.8121 (tttm) outliers start: 56 outliers final: 31 residues processed: 350 average time/residue: 1.4174 time to fit residues: 533.0777 Evaluate side-chains 355 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 313 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 GLU 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 432 MET Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 THR 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 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 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 429 LEU Chi-restraints excluded: chain B residue 431 LEU 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 120 optimal weight: 0.4980 chunk 142 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 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 356 HIS A 50 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 = 0.3695 r_free = 0.3695 target = 0.125554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111095 restraints weight = 16376.169| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.98 r_work: 0.3384 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12170 Z= 0.230 Angle : 0.569 8.933 16471 Z= 0.299 Chirality : 0.043 0.198 1830 Planarity : 0.004 0.042 2110 Dihedral : 7.339 112.378 2024 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.63 % Allowed : 33.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1454 helix: 2.61 (0.26), residues: 378 sheet: 0.19 (0.33), residues: 273 loop : -1.64 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 422 HIS 0.012 0.001 HIS C 356 PHE 0.021 0.001 PHE A 339 TYR 0.012 0.001 TYR B 12 ARG 0.007 0.000 ARG C 74 ********************** 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 361 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 314 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8239 (t) REVERT: C 280 THR cc_start: 0.8549 (p) cc_final: 0.8340 (t) REVERT: C 387 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: C 432 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7208 (mpp) REVERT: C 436 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7478 (mpp80) REVERT: C 452 VAL cc_start: 0.8463 (t) cc_final: 0.8233 (p) REVERT: C 457 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6370 (ttm170) REVERT: C 458 ASP cc_start: 0.7565 (t0) cc_final: 0.7181 (t0) REVERT: A 26 GLU cc_start: 0.7685 (tp30) cc_final: 0.7468 (tp30) REVERT: A 80 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: A 137 MET cc_start: 0.8583 (mmm) cc_final: 0.8232 (mmt) REVERT: A 142 SER cc_start: 0.8235 (p) cc_final: 0.7953 (t) REVERT: A 389 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7367 (mmt) REVERT: A 458 ASP cc_start: 0.8135 (t0) cc_final: 0.7743 (t0) REVERT: A 491 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8129 (ttpp) REVERT: B 27 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6424 (mpt90) REVERT: B 41 THR cc_start: 0.8740 (p) cc_final: 0.8493 (t) REVERT: B 151 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8092 (mmt) REVERT: B 187 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7439 (p0) REVERT: B 451 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7999 (ttmm) REVERT: B 463 LEU cc_start: 0.8776 (mp) cc_final: 0.8507 (mt) REVERT: B 479 MET cc_start: 0.7474 (mmt) cc_final: 0.7027 (mmt) REVERT: B 491 LYS cc_start: 0.8451 (tttm) cc_final: 0.8088 (tttm) REVERT: B 497 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8048 (tmtm) outliers start: 47 outliers final: 28 residues processed: 335 average time/residue: 1.4143 time to fit residues: 508.2565 Evaluate side-chains 353 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 313 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 432 MET Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 139 CYS 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 389 MET 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 313 GLU Chi-restraints excluded: chain B residue 321 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 497 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 0.0370 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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 50 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 480 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.123220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108825 restraints weight = 16472.458| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.95 r_work: 0.3389 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12170 Z= 0.237 Angle : 0.569 8.608 16471 Z= 0.299 Chirality : 0.043 0.198 1830 Planarity : 0.004 0.047 2110 Dihedral : 7.268 113.017 2024 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.87 % Allowed : 33.80 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1454 helix: 2.60 (0.26), residues: 378 sheet: 0.20 (0.33), residues: 273 loop : -1.64 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 65 HIS 0.011 0.001 HIS C 356 PHE 0.031 0.002 PHE B 339 TYR 0.012 0.001 TYR B 12 ARG 0.007 0.000 ARG C 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10632.57 seconds wall clock time: 188 minutes 37.83 seconds (11317.83 seconds total)