Starting phenix.real_space_refine on Wed May 14 12:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xr7_38597/05_2025/8xr7_38597.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xr7_38597/05_2025/8xr7_38597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xr7_38597/05_2025/8xr7_38597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xr7_38597/05_2025/8xr7_38597.map" model { file = "/net/cci-nas-00/data/ceres_data/8xr7_38597/05_2025/8xr7_38597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xr7_38597/05_2025/8xr7_38597.cif" } resolution = 2.62 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 7426 2.51 5 N 2006 2.21 5 O 2305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11812 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3886 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.43, per 1000 atoms: 0.63 Number of scatterers: 11812 At special positions: 0 Unit cell: (87.55, 87.55, 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 2305 8.00 N 2006 7.00 C 7426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 467 " distance=2.03 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=2.02 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=2.02 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 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.03 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 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 NAG-ASN " NAG A 601 " - " ASN A 16 " " NAG A 602 " - " ASN A 28 " " NAG A 603 " - " ASN A 169 " " NAG A 604 " - " ASN A 290 " " NAG A 605 " - " ASN A 484 " " NAG B 601 " - " ASN B 16 " " NAG B 602 " - " ASN B 28 " " NAG B 603 " - " ASN B 169 " " NAG C 701 " - " ASN C 28 " " NAG C 702 " - " ASN C 169 " " NAG C 703 " - " ASN C 290 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 32 sheets defined 27.9% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.928A pdb=" N LEU A 75 " --> pdb=" O CYS A 72 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.880A 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 367 through 387 Processing helix chain 'A' and resid 404 through 457 Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 73 removed outlier: 4.070A pdb=" N ASP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.544A 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 387 Processing helix chain 'B' and resid 404 through 457 removed outlier: 3.590A pdb=" N GLU B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 492 through 502 Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.800A pdb=" N LEU C 75 " --> pdb=" O CYS C 72 " (cutoff:3.500A) removed outlier: 3.828A 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 110 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.843A pdb=" N TRP C 127 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 368 through 389 removed outlier: 4.296A pdb=" N MET C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 457 removed outlier: 3.631A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.704A pdb=" N ASN C 484 " --> pdb=" O ASP C 480 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 502 removed outlier: 3.683A pdb=" N TYR C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU C 494 " --> pdb=" O PRO C 490 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU C 495 " --> pdb=" O LYS C 491 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU C 502 " --> pdb=" O LEU C 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 362 through 364 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.613A pdb=" N LYS A 48 " --> pdb=" O THR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.525A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.398A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS A 115 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG A 263 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 113 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.809A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.721A pdb=" N ALA A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 9.891A pdb=" N LYS A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 4.164A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 363 through 364 Processing sheet with id=AB4, first strand: chain 'B' and resid 19 through 22 removed outlier: 4.314A pdb=" N GLU B 19 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AB6, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.126A pdb=" N LEU B 46 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N CYS B 278 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.627A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.496A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS B 115 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG B 263 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 113 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 100 removed outlier: 7.866A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.481A pdb=" N ALA B 138 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N LYS B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AC3, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AC4, first strand: chain 'C' and resid 362 through 364 removed outlier: 3.575A pdb=" N GLN C 7 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AC6, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AC7, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AC8, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.134A pdb=" N LEU C 46 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.508A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.598A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS C 115 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG C 263 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 113 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.598A pdb=" N SER C 99 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TRP C 234 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.629A pdb=" N ALA C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 10.193A pdb=" N LYS C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD5, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.233A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3865 1.35 - 1.47: 2906 1.47 - 1.59: 5194 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 12079 Sorted by residual: bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG C 703 " pdb=" O5 NAG C 703 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.70e+00 ... (remaining 12074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 16161 2.47 - 4.94: 160 4.94 - 7.41: 11 7.41 - 9.88: 1 9.88 - 12.35: 1 Bond angle restraints: 16334 Sorted by residual: angle pdb=" CA LEU A 419 " pdb=" CB LEU A 419 " pdb=" CG LEU A 419 " ideal model delta sigma weight residual 116.30 128.65 -12.35 3.50e+00 8.16e-02 1.24e+01 angle pdb=" CA GLU C 495 " pdb=" CB GLU C 495 " pdb=" CG GLU C 495 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU B 469 " pdb=" CB GLU B 469 " pdb=" CG GLU B 469 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" N CYS A 139 " pdb=" CA CYS A 139 " pdb=" C CYS A 139 " ideal model delta sigma weight residual 109.71 105.59 4.12 1.41e+00 5.03e-01 8.56e+00 angle pdb=" CB GLU B 469 " pdb=" CG GLU B 469 " pdb=" CD GLU B 469 " ideal model delta sigma weight residual 112.60 117.39 -4.79 1.70e+00 3.46e-01 7.93e+00 ... (remaining 16329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6097 17.94 - 35.89: 886 35.89 - 53.83: 341 53.83 - 71.78: 70 71.78 - 89.72: 16 Dihedral angle restraints: 7410 sinusoidal: 3195 harmonic: 4215 Sorted by residual: dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 72 " pdb=" CB CYS A 72 " ideal model delta sinusoidal sigma weight residual -86.00 -165.24 79.24 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CA CYS A 139 " pdb=" C CYS A 139 " pdb=" N ALA A 140 " pdb=" CA ALA A 140 " ideal model delta harmonic sigma weight residual -180.00 -161.06 -18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA CYS A 72 " pdb=" C CYS A 72 " pdb=" N ASP A 73 " pdb=" CA ASP A 73 " ideal model delta harmonic sigma weight residual -180.00 -161.53 -18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 7407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1168 0.038 - 0.075: 432 0.075 - 0.113: 141 0.113 - 0.151: 29 0.151 - 0.189: 1 Chirality restraints: 1771 Sorted by residual: chirality pdb=" CA CYS A 139 " pdb=" N CYS A 139 " pdb=" C CYS A 139 " pdb=" CB CYS A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CG LEU A 419 " pdb=" CB LEU A 419 " pdb=" CD1 LEU A 419 " pdb=" CD2 LEU A 419 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CG LEU A 429 " pdb=" CB LEU A 429 " pdb=" CD1 LEU A 429 " pdb=" CD2 LEU A 429 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1768 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 158 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO B 159 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 489 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A 490 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 469 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" CD GLU B 469 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU B 469 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 469 " -0.012 2.00e-02 2.50e+03 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1880 2.76 - 3.30: 10047 3.30 - 3.83: 19068 3.83 - 4.37: 22191 4.37 - 4.90: 39828 Nonbonded interactions: 93014 Sorted by model distance: nonbonded pdb=" OG SER A 207 " pdb=" OD1 ASP A 241 " model vdw 2.229 3.040 nonbonded pdb=" O TYR C 195 " pdb=" NZ LYS C 197 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASN B 380 " pdb=" NH2 ARG C 27 " model vdw 2.281 3.120 nonbonded pdb=" O SER C 142 " pdb=" OG SER C 142 " model vdw 2.283 3.040 nonbonded pdb=" N GLU C 495 " pdb=" OE1 GLU C 495 " model vdw 2.289 3.120 ... (remaining 93009 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 502 or resid 601 through 603)) selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.950 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.005 0.041 12108 Z= 0.199 Angle : 0.612 12.346 16403 Z= 0.320 Chirality : 0.044 0.189 1771 Planarity : 0.005 0.064 2105 Dihedral : 19.422 89.721 4662 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.66 % Allowed : 32.56 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1452 helix: 2.10 (0.27), residues: 375 sheet: 0.36 (0.30), residues: 315 loop : -1.91 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.011 0.001 HIS A 356 PHE 0.022 0.002 PHE C 440 TYR 0.022 0.002 TYR B 424 ARG 0.012 0.001 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 11) link_NAG-ASN : angle 1.25542 ( 33) hydrogen bonds : bond 0.18005 ( 463) hydrogen bonds : angle 6.80408 ( 1392) SS BOND : bond 0.00511 ( 18) SS BOND : angle 1.57862 ( 36) covalent geometry : bond 0.00453 (12079) covalent geometry : angle 0.60663 (16334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 377 time to evaluate : 1.277 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 431 LEU cc_start: 0.8608 (mp) cc_final: 0.8387 (mt) outliers start: 60 outliers final: 57 residues processed: 420 average time/residue: 1.3396 time to fit residues: 603.5723 Evaluate side-chains 428 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 371 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 50 ASN A 283 GLN B 175 GLN B 186 ASN B 355 HIS B 356 HIS C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.120479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108761 restraints weight = 15884.055| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.92 r_work: 0.3333 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12108 Z= 0.227 Angle : 0.579 7.936 16403 Z= 0.311 Chirality : 0.045 0.142 1771 Planarity : 0.005 0.048 2105 Dihedral : 9.080 78.101 1903 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.98 % Allowed : 28.13 % Favored : 65.89 % 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: -0.36 (0.21), residues: 1452 helix: 2.14 (0.27), residues: 378 sheet: 0.82 (0.31), residues: 276 loop : -1.96 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 81 HIS 0.011 0.001 HIS A 356 PHE 0.025 0.002 PHE C 440 TYR 0.017 0.002 TYR A 12 ARG 0.009 0.001 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 11) link_NAG-ASN : angle 1.37644 ( 33) hydrogen bonds : bond 0.05822 ( 463) hydrogen bonds : angle 5.07719 ( 1392) SS BOND : bond 0.00431 ( 18) SS BOND : angle 1.30092 ( 36) covalent geometry : bond 0.00538 (12079) covalent geometry : angle 0.57398 (16334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 392 time to evaluate : 1.384 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7584 (ttm110) REVERT: A 212 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.8393 (ttm-80) REVERT: B 272 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: B 276 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: B 491 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8198 (pptt) REVERT: C 47 CYS cc_start: 0.7015 (m) cc_final: 0.6692 (m) outliers start: 77 outliers final: 42 residues processed: 425 average time/residue: 1.3894 time to fit residues: 631.4994 Evaluate side-chains 409 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 363 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 186 ASN B 191 GLN B 356 HIS C 165 GLN C 191 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.120659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108937 restraints weight = 16125.053| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.95 r_work: 0.3339 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12108 Z= 0.170 Angle : 0.541 6.549 16403 Z= 0.291 Chirality : 0.043 0.140 1771 Planarity : 0.005 0.047 2105 Dihedral : 6.900 68.772 1836 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.59 % Allowed : 28.98 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 1452 helix: 2.19 (0.27), residues: 381 sheet: 0.88 (0.31), residues: 279 loop : -1.90 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 81 HIS 0.009 0.001 HIS A 356 PHE 0.020 0.002 PHE C 440 TYR 0.017 0.002 TYR C 92 ARG 0.009 0.001 ARG A 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 11) link_NAG-ASN : angle 1.43103 ( 33) hydrogen bonds : bond 0.05395 ( 463) hydrogen bonds : angle 4.82794 ( 1392) SS BOND : bond 0.00380 ( 18) SS BOND : angle 1.27305 ( 36) covalent geometry : bond 0.00400 (12079) covalent geometry : angle 0.53461 (16334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 369 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8117 (tp) REVERT: A 458 ASP cc_start: 0.8012 (t0) cc_final: 0.7772 (t0) REVERT: B 26 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7592 (mt-10) REVERT: B 111 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8422 (t) REVERT: B 272 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: B 276 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7594 (mt-10) REVERT: B 439 ASP cc_start: 0.7989 (m-30) cc_final: 0.7789 (m-30) REVERT: B 491 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8165 (pptt) REVERT: C 91 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7757 (ttp80) REVERT: C 367 ASP cc_start: 0.8227 (t0) cc_final: 0.8020 (t70) REVERT: C 488 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6287 (t0) outliers start: 72 outliers final: 39 residues processed: 406 average time/residue: 1.2791 time to fit residues: 558.8348 Evaluate side-chains 411 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 366 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 393 PHE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 0.0670 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 326 GLN B 175 GLN B 191 GLN B 356 HIS C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108411 restraints weight = 15991.779| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.94 r_work: 0.3332 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12108 Z= 0.203 Angle : 0.560 6.222 16403 Z= 0.300 Chirality : 0.044 0.140 1771 Planarity : 0.005 0.057 2105 Dihedral : 6.161 56.662 1825 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.83 % Allowed : 28.59 % Favored : 65.58 % 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: -0.26 (0.21), residues: 1452 helix: 2.28 (0.27), residues: 378 sheet: 0.88 (0.31), residues: 279 loop : -1.93 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 81 HIS 0.014 0.001 HIS A 356 PHE 0.023 0.002 PHE C 440 TYR 0.017 0.002 TYR B 424 ARG 0.010 0.001 ARG B 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 11) link_NAG-ASN : angle 1.48377 ( 33) hydrogen bonds : bond 0.05471 ( 463) hydrogen bonds : angle 4.77434 ( 1392) SS BOND : bond 0.00443 ( 18) SS BOND : angle 1.63907 ( 36) covalent geometry : bond 0.00483 (12079) covalent geometry : angle 0.55163 (16334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 377 time to evaluate : 1.292 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8146 (tp) REVERT: B 26 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7544 (mt-10) REVERT: B 272 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: B 276 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: B 439 ASP cc_start: 0.8001 (m-30) cc_final: 0.7786 (m-30) REVERT: B 477 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 491 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8147 (pptt) REVERT: C 91 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7746 (ttp80) REVERT: C 92 TYR cc_start: 0.7593 (m-80) cc_final: 0.6725 (m-80) REVERT: C 367 ASP cc_start: 0.8217 (t0) cc_final: 0.8009 (t70) REVERT: C 389 MET cc_start: 0.8157 (tpp) cc_final: 0.7922 (tpp) REVERT: C 488 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.6263 (t0) outliers start: 75 outliers final: 45 residues processed: 411 average time/residue: 1.2523 time to fit residues: 553.9107 Evaluate side-chains 410 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 107 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 191 GLN B 356 HIS C 191 GLN C 224 ASN ** C 296 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 = 0.3641 r_free = 0.3641 target = 0.120238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108548 restraints weight = 15897.421| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.93 r_work: 0.3337 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12108 Z= 0.206 Angle : 0.567 6.500 16403 Z= 0.303 Chirality : 0.044 0.142 1771 Planarity : 0.004 0.044 2105 Dihedral : 5.855 54.754 1820 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.91 % Allowed : 28.75 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1452 helix: 2.20 (0.27), residues: 381 sheet: 0.72 (0.31), residues: 285 loop : -1.90 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 81 HIS 0.013 0.001 HIS A 356 PHE 0.023 0.002 PHE C 440 TYR 0.017 0.002 TYR B 424 ARG 0.008 0.001 ARG B 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 11) link_NAG-ASN : angle 1.47756 ( 33) hydrogen bonds : bond 0.05454 ( 463) hydrogen bonds : angle 4.76701 ( 1392) SS BOND : bond 0.00458 ( 18) SS BOND : angle 1.81971 ( 36) covalent geometry : bond 0.00493 (12079) covalent geometry : angle 0.55762 (16334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 375 time to evaluate : 1.239 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8160 (tp) REVERT: A 458 ASP cc_start: 0.8098 (t0) cc_final: 0.7676 (t0) REVERT: B 26 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7540 (mt-10) REVERT: B 118 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8627 (mtpt) REVERT: B 272 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: B 276 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: B 439 ASP cc_start: 0.7983 (m-30) cc_final: 0.7653 (m-30) REVERT: B 477 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7890 (tm-30) REVERT: B 491 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8146 (pptt) REVERT: C 91 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7686 (ttp80) REVERT: C 278 CYS cc_start: 0.6142 (p) cc_final: 0.5833 (p) REVERT: C 389 MET cc_start: 0.8180 (tpp) cc_final: 0.7943 (tpp) REVERT: C 488 ASP cc_start: 0.6563 (OUTLIER) cc_final: 0.6251 (t0) outliers start: 76 outliers final: 49 residues processed: 409 average time/residue: 1.3094 time to fit residues: 574.8462 Evaluate side-chains 426 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 371 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 114 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 326 GLN B 175 GLN B 191 GLN B 356 HIS C 191 GLN C 196 GLN C 224 ASN C 244 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108729 restraints weight = 16187.399| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3353 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12108 Z= 0.184 Angle : 0.558 7.005 16403 Z= 0.299 Chirality : 0.043 0.142 1771 Planarity : 0.004 0.043 2105 Dihedral : 5.624 51.713 1820 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.83 % Allowed : 29.68 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1452 helix: 2.30 (0.27), residues: 378 sheet: 0.75 (0.31), residues: 285 loop : -1.89 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 81 HIS 0.012 0.001 HIS A 356 PHE 0.021 0.002 PHE C 440 TYR 0.018 0.002 TYR B 424 ARG 0.010 0.001 ARG B 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 11) link_NAG-ASN : angle 1.46278 ( 33) hydrogen bonds : bond 0.05307 ( 463) hydrogen bonds : angle 4.72642 ( 1392) SS BOND : bond 0.00445 ( 18) SS BOND : angle 1.66787 ( 36) covalent geometry : bond 0.00438 (12079) covalent geometry : angle 0.55006 (16334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 380 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8251 (mtmm) cc_final: 0.8033 (mtmm) REVERT: A 394 GLU cc_start: -0.0238 (OUTLIER) cc_final: -0.0558 (pp20) REVERT: A 428 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8147 (tp) REVERT: A 458 ASP cc_start: 0.8120 (t0) cc_final: 0.7715 (t0) REVERT: B 26 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 71 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7102 (mt-10) REVERT: B 74 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8306 (mtm-85) REVERT: B 92 TYR cc_start: 0.6780 (m-10) cc_final: 0.6470 (m-10) REVERT: B 118 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8640 (mtpt) REVERT: B 272 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 276 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: B 439 ASP cc_start: 0.8034 (m-30) cc_final: 0.7832 (m-30) REVERT: B 477 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7922 (tm-30) REVERT: B 491 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8205 (pptt) REVERT: C 47 CYS cc_start: 0.6972 (m) cc_final: 0.6694 (m) REVERT: C 91 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7735 (ttp80) REVERT: C 389 MET cc_start: 0.8189 (tpp) cc_final: 0.7935 (tpp) REVERT: C 458 ASP cc_start: 0.7897 (t0) cc_final: 0.7526 (t0) REVERT: C 488 ASP cc_start: 0.6610 (OUTLIER) cc_final: 0.6292 (t0) outliers start: 75 outliers final: 50 residues processed: 414 average time/residue: 1.4017 time to fit residues: 623.0194 Evaluate side-chains 427 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 369 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 488 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 191 GLN B 356 HIS C 191 GLN C 224 ASN ** C 296 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 = 0.3645 r_free = 0.3645 target = 0.120423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108691 restraints weight = 16104.794| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.94 r_work: 0.3352 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12108 Z= 0.185 Angle : 0.571 9.951 16403 Z= 0.302 Chirality : 0.043 0.144 1771 Planarity : 0.004 0.043 2105 Dihedral : 5.449 46.827 1819 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.75 % Allowed : 30.38 % Favored : 63.87 % 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: -0.24 (0.21), residues: 1452 helix: 2.26 (0.27), residues: 381 sheet: 0.75 (0.31), residues: 285 loop : -1.88 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 422 HIS 0.011 0.001 HIS A 356 PHE 0.022 0.002 PHE B 295 TYR 0.020 0.002 TYR B 424 ARG 0.010 0.001 ARG B 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00214 ( 11) link_NAG-ASN : angle 1.46684 ( 33) hydrogen bonds : bond 0.05284 ( 463) hydrogen bonds : angle 4.70387 ( 1392) SS BOND : bond 0.00517 ( 18) SS BOND : angle 1.84807 ( 36) covalent geometry : bond 0.00441 (12079) covalent geometry : angle 0.56177 (16334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 370 time to evaluate : 1.270 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7273 (mpt90) REVERT: A 394 GLU cc_start: -0.0128 (OUTLIER) cc_final: -0.0413 (pp20) REVERT: A 428 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8147 (tp) REVERT: A 458 ASP cc_start: 0.8160 (t0) cc_final: 0.7777 (t0) REVERT: B 26 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 71 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7091 (mt-10) REVERT: B 74 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8308 (mtm-85) REVERT: B 92 TYR cc_start: 0.6794 (m-10) cc_final: 0.6456 (m-10) REVERT: B 118 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8633 (mtpt) REVERT: B 272 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: B 276 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: B 477 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7950 (tm-30) REVERT: B 491 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8177 (pptt) REVERT: C 389 MET cc_start: 0.8203 (tpp) cc_final: 0.7945 (tpp) REVERT: C 458 ASP cc_start: 0.7882 (t0) cc_final: 0.7442 (t0) outliers start: 74 outliers final: 47 residues processed: 405 average time/residue: 1.3009 time to fit residues: 564.8819 Evaluate side-chains 416 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 361 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 0.4980 chunk 103 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.0970 chunk 123 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 175 GLN B 191 GLN B 356 HIS B 360 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.121838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.110095 restraints weight = 16018.910| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.94 r_work: 0.3374 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12108 Z= 0.124 Angle : 0.552 13.297 16403 Z= 0.290 Chirality : 0.042 0.198 1771 Planarity : 0.004 0.043 2105 Dihedral : 5.153 46.280 1817 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.82 % Allowed : 31.62 % Favored : 63.56 % 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: -0.13 (0.22), residues: 1452 helix: 2.40 (0.27), residues: 381 sheet: 0.56 (0.31), residues: 297 loop : -1.76 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 422 HIS 0.010 0.001 HIS A 356 PHE 0.025 0.001 PHE B 295 TYR 0.021 0.001 TYR B 424 ARG 0.009 0.001 ARG C 91 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 11) link_NAG-ASN : angle 1.41579 ( 33) hydrogen bonds : bond 0.04806 ( 463) hydrogen bonds : angle 4.59779 ( 1392) SS BOND : bond 0.00401 ( 18) SS BOND : angle 1.70759 ( 36) covalent geometry : bond 0.00289 (12079) covalent geometry : angle 0.54353 (16334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 364 time to evaluate : 1.365 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: symmetry clash REVERT: A 20 LYS cc_start: 0.8274 (mptp) cc_final: 0.8065 (mptp) REVERT: A 27 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7260 (mpt90) REVERT: A 394 GLU cc_start: -0.0069 (OUTLIER) cc_final: -0.0358 (pp20) REVERT: A 428 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8088 (tp) REVERT: A 458 ASP cc_start: 0.8184 (t0) cc_final: 0.7724 (t0) REVERT: B 26 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7579 (mt-10) REVERT: B 71 GLU cc_start: 0.8342 (mt-10) cc_final: 0.6966 (mt-10) REVERT: B 74 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8325 (mtm-85) REVERT: B 92 TYR cc_start: 0.6689 (m-10) cc_final: 0.6391 (m-10) REVERT: B 111 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8429 (t) REVERT: B 118 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8616 (mtpt) REVERT: B 276 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: B 477 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 491 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8186 (pptt) REVERT: C 91 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7524 (ttp80) REVERT: C 144 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7547 (mppt) REVERT: C 389 MET cc_start: 0.8148 (tpp) cc_final: 0.7886 (tpp) REVERT: C 458 ASP cc_start: 0.7882 (t0) cc_final: 0.7531 (t0) outliers start: 62 outliers final: 40 residues processed: 392 average time/residue: 1.2188 time to fit residues: 515.0362 Evaluate side-chains 419 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 370 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 0.0470 chunk 118 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN A 196 GLN B 175 GLN B 356 HIS B 372 GLN C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.121515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109699 restraints weight = 16111.760| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.95 r_work: 0.3351 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12108 Z= 0.152 Angle : 0.586 16.666 16403 Z= 0.305 Chirality : 0.043 0.249 1771 Planarity : 0.004 0.043 2105 Dihedral : 4.993 46.203 1815 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.43 % Allowed : 33.02 % Favored : 62.55 % 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: -0.13 (0.22), residues: 1452 helix: 2.37 (0.27), residues: 381 sheet: 0.57 (0.31), residues: 297 loop : -1.74 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 422 HIS 0.013 0.001 HIS A 356 PHE 0.026 0.002 PHE B 295 TYR 0.023 0.001 TYR B 424 ARG 0.011 0.001 ARG B 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 11) link_NAG-ASN : angle 1.49530 ( 33) hydrogen bonds : bond 0.04954 ( 463) hydrogen bonds : angle 4.59530 ( 1392) SS BOND : bond 0.00467 ( 18) SS BOND : angle 1.87222 ( 36) covalent geometry : bond 0.00360 (12079) covalent geometry : angle 0.57714 (16334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 365 time to evaluate : 1.396 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: A 27 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7291 (mpt90) REVERT: A 190 GLU cc_start: 0.8247 (pt0) cc_final: 0.7979 (pt0) REVERT: A 394 GLU cc_start: -0.0011 (OUTLIER) cc_final: -0.0314 (pp20) REVERT: A 404 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 428 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8102 (tp) REVERT: A 458 ASP cc_start: 0.8178 (t0) cc_final: 0.7819 (t0) REVERT: B 26 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7548 (mt-10) REVERT: B 71 GLU cc_start: 0.8323 (mt-10) cc_final: 0.6921 (mt-10) REVERT: B 74 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8310 (mtm-85) REVERT: B 92 TYR cc_start: 0.6708 (m-10) cc_final: 0.6436 (m-10) REVERT: B 111 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8432 (t) REVERT: B 118 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8627 (mtpt) REVERT: B 276 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: B 477 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 491 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8171 (pptt) REVERT: C 39 GLU cc_start: 0.7865 (tp30) cc_final: 0.7626 (tp30) REVERT: C 91 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7651 (ttp80) REVERT: C 144 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7645 (mppt) REVERT: C 389 MET cc_start: 0.8095 (tpp) cc_final: 0.7853 (tpp) REVERT: C 458 ASP cc_start: 0.7931 (t0) cc_final: 0.7474 (t0) outliers start: 57 outliers final: 40 residues processed: 392 average time/residue: 1.2889 time to fit residues: 543.5378 Evaluate side-chains 411 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 362 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 126 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 356 HIS B 372 GLN C 165 GLN C 191 GLN C 196 GLN C 224 ASN C 390 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108935 restraints weight = 16061.131| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.95 r_work: 0.3342 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12108 Z= 0.206 Angle : 0.625 16.637 16403 Z= 0.326 Chirality : 0.045 0.261 1771 Planarity : 0.004 0.043 2105 Dihedral : 4.997 46.113 1815 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.89 % Allowed : 33.57 % Favored : 62.55 % 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: -0.20 (0.21), residues: 1452 helix: 2.22 (0.27), residues: 381 sheet: 0.81 (0.31), residues: 285 loop : -1.83 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 65 HIS 0.014 0.001 HIS A 356 PHE 0.029 0.002 PHE B 295 TYR 0.027 0.002 TYR B 424 ARG 0.011 0.001 ARG B 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 11) link_NAG-ASN : angle 1.63921 ( 33) hydrogen bonds : bond 0.05335 ( 463) hydrogen bonds : angle 4.68031 ( 1392) SS BOND : bond 0.00568 ( 18) SS BOND : angle 2.07992 ( 36) covalent geometry : bond 0.00495 (12079) covalent geometry : angle 0.61406 (16334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 367 time to evaluate : 1.257 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: symmetry clash REVERT: A 27 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7287 (mpt90) REVERT: A 94 LEU cc_start: 0.8719 (mt) cc_final: 0.8513 (mp) REVERT: A 190 GLU cc_start: 0.8250 (pt0) cc_final: 0.7990 (pt0) REVERT: A 394 GLU cc_start: -0.0080 (OUTLIER) cc_final: -0.0401 (pp20) REVERT: A 404 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 428 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8160 (tp) REVERT: A 458 ASP cc_start: 0.8173 (t0) cc_final: 0.7812 (t0) REVERT: B 26 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 71 GLU cc_start: 0.8326 (mt-10) cc_final: 0.6890 (mt-10) REVERT: B 74 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8283 (mtm-85) REVERT: B 92 TYR cc_start: 0.6754 (m-10) cc_final: 0.6462 (m-10) REVERT: B 111 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8419 (t) REVERT: B 118 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8635 (mtpt) REVERT: B 276 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: B 477 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7952 (tm-30) REVERT: B 491 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8213 (pptt) REVERT: C 91 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7692 (ttp80) REVERT: C 144 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7666 (mppt) REVERT: C 389 MET cc_start: 0.8079 (tpp) cc_final: 0.7800 (tpp) REVERT: C 458 ASP cc_start: 0.7945 (t0) cc_final: 0.7492 (t0) outliers start: 50 outliers final: 38 residues processed: 390 average time/residue: 1.3001 time to fit residues: 544.5765 Evaluate side-chains 400 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 353 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 27 ARG Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 74 ARG Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 380 ASN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 491 LYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 446 LYS Chi-restraints excluded: chain C residue 478 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS A 165 GLN B 356 HIS B 372 GLN C 165 GLN C 191 GLN C 196 GLN C 224 ASN ** C 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109789 restraints weight = 15905.113| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.94 r_work: 0.3352 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12108 Z= 0.162 Angle : 0.583 10.571 16403 Z= 0.308 Chirality : 0.044 0.202 1771 Planarity : 0.004 0.042 2105 Dihedral : 4.912 46.551 1815 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.96 % Allowed : 33.33 % Favored : 62.70 % 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: -0.20 (0.22), residues: 1452 helix: 2.26 (0.27), residues: 381 sheet: 0.54 (0.30), residues: 297 loop : -1.76 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.013 0.001 HIS A 356 PHE 0.028 0.002 PHE B 295 TYR 0.025 0.002 TYR B 424 ARG 0.011 0.001 ARG B 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 11) link_NAG-ASN : angle 1.50608 ( 33) hydrogen bonds : bond 0.05067 ( 463) hydrogen bonds : angle 4.63453 ( 1392) SS BOND : bond 0.00490 ( 18) SS BOND : angle 1.73433 ( 36) covalent geometry : bond 0.00385 (12079) covalent geometry : angle 0.57486 (16334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11192.60 seconds wall clock time: 193 minutes 6.10 seconds (11586.10 seconds total)