Starting phenix.real_space_refine on Mon Dec 30 00:17:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xhf_38349/12_2024/8xhf_38349.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xhf_38349/12_2024/8xhf_38349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xhf_38349/12_2024/8xhf_38349.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xhf_38349/12_2024/8xhf_38349.map" model { file = "/net/cci-nas-00/data/ceres_data/8xhf_38349/12_2024/8xhf_38349.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xhf_38349/12_2024/8xhf_38349.cif" } resolution = 2.39 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= 0.025 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 7356 2.51 5 N 2001 2.21 5 O 2304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11736 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3870 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 19, 'TRANS': 468} Chain breaks: 1 Chain: "A" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3870 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 19, 'TRANS': 468} Chain breaks: 1 Chain: "B" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3870 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 19, 'TRANS': 468} Chain breaks: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.86, per 1000 atoms: 0.67 Number of scatterers: 11736 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 2304 8.00 N 2001 7.00 C 7356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 467 " distance=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 139 " distance=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 72 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 478 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 169 " " NAG A 602 " - " ASN A 484 " " NAG A 603 " - " ASN A 28 " " NAG B 601 " - " ASN B 169 " " NAG B 602 " - " ASN B 28 " " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 28 " " NAG C 603 " - " ASN C 484 " " NAG C 604 " - " ASN C 290 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.6 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: 2682 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 33 sheets defined 28.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.787A 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 387 Processing helix chain 'C' and resid 404 through 457 removed outlier: 3.702A pdb=" N GLU C 435 " --> pdb=" O LEU C 431 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.901A pdb=" N ASP A 73 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.801A 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 338 through 342 removed outlier: 3.645A pdb=" N GLU A 341 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 388 Processing helix chain 'A' and resid 404 through 457 removed outlier: 3.780A pdb=" N ASP A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.554A pdb=" N LEU A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.915A pdb=" N ASP B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 367 through 388 removed outlier: 3.619A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 457 removed outlier: 3.623A pdb=" N ASP B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 445 " --> pdb=" O HIS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 488 through 500 removed outlier: 4.515A pdb=" N TYR B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLU B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN B 499 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 363 through 364 removed outlier: 3.587A pdb=" N GLY C 11 " --> pdb=" O GLY C 353 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.366A pdb=" N LEU C 46 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.641A pdb=" N LEU C 55 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE C 84 " --> pdb=" O MET C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.344A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS C 115 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG C 263 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 113 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 98 through 100 removed outlier: 7.909A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.921A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB1, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.316A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 366 removed outlier: 3.730A pdb=" N GLY A 361 " --> pdb=" O ASN A 358 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 356 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 11 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AB6, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AB7, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.061A pdb=" N LYS A 48 " --> pdb=" O THR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.603A pdb=" N LEU A 55 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 84 " --> pdb=" O MET A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.470A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 98 through 100 removed outlier: 7.899A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AC3, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.885A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AC6, first strand: chain 'B' and resid 362 through 364 removed outlier: 3.565A pdb=" N GLY B 11 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 7 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AC8, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AC9, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AD1, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.623A pdb=" N LEU B 55 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE B 84 " --> pdb=" O MET B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.654A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 98 through 100 removed outlier: 6.654A pdb=" N SER B 99 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP B 234 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 136 through 141 removed outlier: 4.519A pdb=" N CYS B 139 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 146 " --> pdb=" O CYS B 139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'B' and resid 287 through 289 removed outlier: 4.588A pdb=" N CYS B 282 " --> pdb=" O ILE B 289 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3866 1.34 - 1.46: 2822 1.46 - 1.58: 5192 1.58 - 1.70: 0 1.70 - 1.83: 114 Bond restraints: 11994 Sorted by residual: bond pdb=" C TYR B 489 " pdb=" N PRO B 490 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.46e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C1 NAG C 604 " pdb=" O5 NAG C 604 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" CB LYS B 473 " pdb=" CG LYS B 473 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 ... (remaining 11989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15879 1.55 - 3.10: 308 3.10 - 4.64: 31 4.64 - 6.19: 7 6.19 - 7.74: 2 Bond angle restraints: 16227 Sorted by residual: angle pdb=" C ARG C 457 " pdb=" CA ARG C 457 " pdb=" CB ARG C 457 " ideal model delta sigma weight residual 116.63 110.29 6.34 1.16e+00 7.43e-01 2.99e+01 angle pdb=" CB LYS B 473 " pdb=" CG LYS B 473 " pdb=" CD LYS B 473 " ideal model delta sigma weight residual 111.30 119.04 -7.74 2.30e+00 1.89e-01 1.13e+01 angle pdb=" CA ARG C 457 " pdb=" C ARG C 457 " pdb=" N ASP C 458 " ideal model delta sigma weight residual 119.63 117.05 2.58 8.10e-01 1.52e+00 1.02e+01 angle pdb=" N ARG C 457 " pdb=" CA ARG C 457 " pdb=" C ARG C 457 " ideal model delta sigma weight residual 108.08 112.66 -4.58 1.69e+00 3.50e-01 7.35e+00 angle pdb=" CA CYS B 278 " pdb=" CB CYS B 278 " pdb=" SG CYS B 278 " ideal model delta sigma weight residual 114.40 120.32 -5.92 2.30e+00 1.89e-01 6.63e+00 ... (remaining 16222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 6066 18.22 - 36.43: 879 36.43 - 54.65: 301 54.65 - 72.86: 51 72.86 - 91.08: 20 Dihedral angle restraints: 7317 sinusoidal: 3120 harmonic: 4197 Sorted by residual: dihedral pdb=" CB CYS B 47 " pdb=" SG CYS B 47 " pdb=" SG CYS B 278 " pdb=" CB CYS B 278 " ideal model delta sinusoidal sigma weight residual -86.00 -12.07 -73.93 1 1.00e+01 1.00e-02 6.94e+01 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 93.00 132.51 -39.51 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N CYS B 47 " pdb=" CA CYS B 47 " ideal model delta harmonic sigma weight residual -180.00 -159.90 -20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1446 0.052 - 0.105: 256 0.105 - 0.157: 67 0.157 - 0.210: 0 0.210 - 0.262: 1 Chirality restraints: 1770 Sorted by residual: chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 28 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO B 307 " pdb=" N PRO B 307 " pdb=" C PRO B 307 " pdb=" CB PRO B 307 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 28 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1767 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 339 " 0.011 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE C 339 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE C 339 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 339 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 339 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 339 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 339 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 18 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C THR C 18 " 0.026 2.00e-02 2.50e+03 pdb=" O THR C 18 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU C 19 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 415 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" CD GLU B 415 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU B 415 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU B 415 " 0.008 2.00e-02 2.50e+03 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 976 2.74 - 3.28: 10299 3.28 - 3.82: 18841 3.82 - 4.36: 22641 4.36 - 4.90: 40060 Nonbonded interactions: 92817 Sorted by model distance: nonbonded pdb=" O SER B 112 " pdb=" OG SER B 112 " model vdw 2.199 3.040 nonbonded pdb=" O SER B 142 " pdb=" OG SER B 142 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN C 15 " pdb=" OG SER C 17 " model vdw 2.247 3.040 nonbonded pdb=" O SER C 112 " pdb=" OG SER C 112 " model vdw 2.275 3.040 nonbonded pdb=" O SER A 159 " pdb=" OG SER A 159 " model vdw 2.316 3.040 ... (remaining 92812 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 500 or resid 601 through 602)) selection = chain 'B' selection = (chain 'C' and (resid 6 through 500 or resid 601 through 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.930 Find NCS groups from input model: 0.610 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: 0.000 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11994 Z= 0.256 Angle : 0.526 7.738 16227 Z= 0.279 Chirality : 0.043 0.262 1770 Planarity : 0.004 0.043 2097 Dihedral : 19.113 91.078 4581 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 4.42 % Allowed : 29.53 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1452 helix: 2.16 (0.27), residues: 375 sheet: 0.89 (0.31), residues: 294 loop : -1.59 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 422 HIS 0.012 0.001 HIS C 356 PHE 0.030 0.002 PHE C 339 TYR 0.018 0.001 TYR A 12 ARG 0.010 0.001 ARG A 192 *********************** 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 358 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 301 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 ASP cc_start: 0.7725 (t0) cc_final: 0.7439 (t0) outliers start: 57 outliers final: 50 residues processed: 354 average time/residue: 1.4710 time to fit residues: 556.4114 Evaluate side-chains 347 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 297 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 82 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 345 GLN Chi-restraints excluded: chain C residue 360 GLN Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 392 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 492 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.5980 chunk 109 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.0010 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS C 499 ASN A 380 ASN A 392 GLN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN B 472 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 11994 Z= 0.161 Angle : 0.496 9.580 16227 Z= 0.267 Chirality : 0.041 0.244 1770 Planarity : 0.004 0.031 2097 Dihedral : 8.062 64.854 1845 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.74 % Allowed : 25.66 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1452 helix: 2.50 (0.27), residues: 378 sheet: 0.68 (0.31), residues: 312 loop : -1.30 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.011 0.001 HIS B 472 PHE 0.017 0.001 PHE A 295 TYR 0.012 0.001 TYR A 12 ARG 0.006 0.000 ARG C 126 *********************** 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 394 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 320 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8476 (p) cc_final: 0.8260 (t) REVERT: C 491 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7547 (tttm) REVERT: A 67 LEU cc_start: 0.8861 (mt) cc_final: 0.8558 (mt) REVERT: A 456 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 479 MET cc_start: 0.8054 (tpp) cc_final: 0.7589 (mmp) REVERT: B 491 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7175 (mtpt) outliers start: 74 outliers final: 35 residues processed: 364 average time/residue: 1.4471 time to fit residues: 564.8132 Evaluate side-chains 351 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 313 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 228 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 310 VAL Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 454 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 116 optimal weight: 0.0870 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS C 499 ASN A 380 ASN B 186 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11994 Z= 0.314 Angle : 0.550 11.165 16227 Z= 0.297 Chirality : 0.044 0.279 1770 Planarity : 0.004 0.037 2097 Dihedral : 7.138 84.575 1793 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.56 % Rotamer: Outliers : 5.12 % Allowed : 25.89 % Favored : 68.99 % 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: 0.22 (0.22), residues: 1452 helix: 2.44 (0.27), residues: 378 sheet: 0.52 (0.30), residues: 333 loop : -1.34 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 422 HIS 0.011 0.001 HIS C 356 PHE 0.025 0.002 PHE B 440 TYR 0.022 0.002 TYR A 12 ARG 0.006 0.001 ARG A 192 *********************** 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 378 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 312 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 491 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7589 (tttm) REVERT: A 456 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 436 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7247 (mpp-170) REVERT: B 491 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7192 (mtpt) REVERT: B 497 LYS cc_start: 0.8224 (tppt) cc_final: 0.7905 (tppt) outliers start: 66 outliers final: 36 residues processed: 349 average time/residue: 1.4586 time to fit residues: 545.4007 Evaluate side-chains 349 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 309 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11994 Z= 0.239 Angle : 0.514 9.221 16227 Z= 0.278 Chirality : 0.043 0.279 1770 Planarity : 0.004 0.036 2097 Dihedral : 6.348 56.263 1785 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.96 % Allowed : 25.81 % Favored : 69.22 % 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: 0.28 (0.22), residues: 1452 helix: 2.53 (0.27), residues: 378 sheet: 0.55 (0.30), residues: 333 loop : -1.31 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.011 0.001 HIS C 356 PHE 0.023 0.002 PHE C 339 TYR 0.027 0.001 TYR A 489 ARG 0.007 0.000 ARG A 192 *********************** 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 371 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8505 (p) cc_final: 0.8249 (t) REVERT: A 345 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: A 458 ASP cc_start: 0.7661 (t0) cc_final: 0.7297 (t0) REVERT: B 436 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7236 (mpp-170) REVERT: B 491 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7136 (mtpt) REVERT: B 497 LYS cc_start: 0.8210 (tppt) cc_final: 0.7890 (tppt) outliers start: 64 outliers final: 39 residues processed: 339 average time/residue: 1.4811 time to fit residues: 539.3102 Evaluate side-chains 351 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 309 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 chunk 118 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11994 Z= 0.202 Angle : 0.497 8.233 16227 Z= 0.268 Chirality : 0.042 0.275 1770 Planarity : 0.004 0.036 2097 Dihedral : 5.805 56.522 1775 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.73 % Allowed : 26.90 % Favored : 68.37 % 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: 0.35 (0.22), residues: 1452 helix: 2.62 (0.27), residues: 378 sheet: 0.58 (0.30), residues: 333 loop : -1.28 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.011 0.001 HIS C 356 PHE 0.025 0.001 PHE C 339 TYR 0.028 0.001 TYR A 489 ARG 0.006 0.000 ARG C 126 *********************** 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 373 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 312 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 ARG cc_start: 0.9064 (mtm-85) cc_final: 0.8702 (mtm-85) REVERT: C 302 THR cc_start: 0.8461 (p) cc_final: 0.8231 (t) REVERT: A 345 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7756 (mt0) REVERT: A 456 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8467 (mp) REVERT: A 458 ASP cc_start: 0.7655 (t0) cc_final: 0.7300 (t0) REVERT: A 479 MET cc_start: 0.8076 (tpp) cc_final: 0.7626 (mmp) REVERT: B 436 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7243 (mpp-170) REVERT: B 491 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7135 (mtpt) REVERT: B 497 LYS cc_start: 0.8208 (tppt) cc_final: 0.7900 (tppt) outliers start: 61 outliers final: 37 residues processed: 343 average time/residue: 1.4087 time to fit residues: 520.0728 Evaluate side-chains 347 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 306 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN A 459 ASN B 160 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11994 Z= 0.189 Angle : 0.488 7.926 16227 Z= 0.263 Chirality : 0.042 0.269 1770 Planarity : 0.004 0.036 2097 Dihedral : 5.470 56.197 1771 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.42 % Allowed : 27.21 % Favored : 68.37 % 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 (0.23), residues: 1452 helix: 2.70 (0.27), residues: 378 sheet: 0.63 (0.30), residues: 333 loop : -1.25 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 422 HIS 0.011 0.001 HIS C 356 PHE 0.026 0.001 PHE C 339 TYR 0.029 0.001 TYR A 489 ARG 0.007 0.000 ARG C 126 *********************** 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 365 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 308 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8426 (p) cc_final: 0.8210 (t) REVERT: C 305 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5794 (mp0) REVERT: A 345 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: A 440 PHE cc_start: 0.8328 (t80) cc_final: 0.8022 (t80) REVERT: A 456 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 458 ASP cc_start: 0.7633 (t0) cc_final: 0.7389 (t0) REVERT: A 479 MET cc_start: 0.8082 (tpp) cc_final: 0.7637 (mmp) REVERT: B 436 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7239 (mpp-170) REVERT: B 491 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7109 (mtpt) outliers start: 57 outliers final: 37 residues processed: 339 average time/residue: 1.3460 time to fit residues: 490.2103 Evaluate side-chains 352 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 497 LYS Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 78 optimal weight: 0.2980 chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 ASN C 356 HIS A 380 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11994 Z= 0.190 Angle : 0.493 7.746 16227 Z= 0.265 Chirality : 0.042 0.266 1770 Planarity : 0.004 0.036 2097 Dihedral : 5.364 55.366 1771 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.95 % Allowed : 27.91 % Favored : 68.14 % 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: 0.46 (0.23), residues: 1452 helix: 2.70 (0.27), residues: 378 sheet: 0.68 (0.30), residues: 333 loop : -1.22 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.011 0.001 HIS C 356 PHE 0.028 0.001 PHE C 339 TYR 0.028 0.001 TYR A 489 ARG 0.007 0.000 ARG C 126 *********************** 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 359 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 302 THR cc_start: 0.8425 (p) cc_final: 0.8214 (t) REVERT: C 305 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5822 (mp0) REVERT: C 479 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7352 (mtt) REVERT: A 345 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: A 456 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 479 MET cc_start: 0.8071 (tpp) cc_final: 0.7656 (mmp) REVERT: B 186 ASN cc_start: 0.8488 (t0) cc_final: 0.8279 (t0) REVERT: B 436 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7243 (mpp-170) REVERT: B 491 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7100 (mtpt) outliers start: 51 outliers final: 36 residues processed: 332 average time/residue: 1.4307 time to fit residues: 509.4895 Evaluate side-chains 348 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 306 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS A 380 ASN B 224 ASN B 244 ASN B 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11994 Z= 0.322 Angle : 0.554 8.575 16227 Z= 0.299 Chirality : 0.045 0.276 1770 Planarity : 0.004 0.038 2097 Dihedral : 5.390 56.367 1767 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 4.03 % Allowed : 27.83 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1452 helix: 2.51 (0.27), residues: 378 sheet: 0.60 (0.30), residues: 333 loop : -1.34 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 65 HIS 0.012 0.001 HIS C 356 PHE 0.029 0.002 PHE C 339 TYR 0.028 0.002 TYR A 489 ARG 0.009 0.001 ARG A 192 *********************** 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 357 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5840 (mp0) REVERT: A 345 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: A 479 MET cc_start: 0.8117 (tpp) cc_final: 0.7809 (mmp) REVERT: B 436 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7248 (mpp-170) REVERT: B 491 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7084 (mtpt) outliers start: 52 outliers final: 33 residues processed: 332 average time/residue: 1.4290 time to fit residues: 508.7306 Evaluate side-chains 334 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 210 ASN 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 292 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 0.0070 chunk 122 optimal weight: 0.0370 chunk 128 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS A 380 ASN B 224 ASN B 296 HIS B 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11994 Z= 0.144 Angle : 0.490 7.128 16227 Z= 0.263 Chirality : 0.041 0.256 1770 Planarity : 0.004 0.035 2097 Dihedral : 4.901 53.943 1765 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.10 % Allowed : 28.76 % Favored : 68.14 % 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: 0.51 (0.23), residues: 1452 helix: 2.75 (0.28), residues: 378 sheet: 0.66 (0.32), residues: 303 loop : -1.10 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 422 HIS 0.012 0.001 HIS C 356 PHE 0.026 0.001 PHE C 339 TYR 0.030 0.001 TYR A 489 ARG 0.008 0.000 ARG A 192 *********************** 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 348 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5934 (mp0) REVERT: C 479 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7349 (mtt) REVERT: A 345 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: A 479 MET cc_start: 0.8039 (tpp) cc_final: 0.7635 (mmp) REVERT: B 436 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7178 (mpp-170) REVERT: B 491 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7071 (mtpt) outliers start: 40 outliers final: 25 residues processed: 327 average time/residue: 1.4107 time to fit residues: 495.7019 Evaluate side-chains 332 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 302 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS A 380 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN B 459 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11994 Z= 0.222 Angle : 0.522 8.784 16227 Z= 0.279 Chirality : 0.043 0.259 1770 Planarity : 0.004 0.037 2097 Dihedral : 4.893 49.923 1763 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.48 % Allowed : 29.69 % Favored : 67.83 % 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: 0.44 (0.22), residues: 1452 helix: 2.69 (0.27), residues: 378 sheet: 0.64 (0.31), residues: 303 loop : -1.15 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 422 HIS 0.015 0.001 HIS C 356 PHE 0.030 0.002 PHE C 339 TYR 0.027 0.001 TYR A 489 ARG 0.008 0.001 ARG A 192 ********************** 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 331 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 299 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5948 (mp0) REVERT: A 345 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: A 389 MET cc_start: 0.7879 (mmm) cc_final: 0.7671 (mtm) REVERT: A 479 MET cc_start: 0.8098 (tpp) cc_final: 0.7692 (mmp) REVERT: B 436 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7218 (mpp-170) REVERT: B 491 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7059 (mtpt) outliers start: 32 outliers final: 22 residues processed: 314 average time/residue: 1.4310 time to fit residues: 481.1630 Evaluate side-chains 324 residues out of total 1290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 298 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 491 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.0030 chunk 100 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 HIS A 380 ASN A 459 ASN B 224 ASN ** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.113477 restraints weight = 15501.667| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.58 r_work: 0.3514 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11994 Z= 0.201 Angle : 0.524 9.534 16227 Z= 0.279 Chirality : 0.042 0.258 1770 Planarity : 0.004 0.048 2097 Dihedral : 4.888 52.552 1762 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.40 % Allowed : 29.77 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1452 helix: 2.68 (0.27), residues: 378 sheet: 0.65 (0.31), residues: 303 loop : -1.14 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 422 HIS 0.016 0.001 HIS C 356 PHE 0.029 0.001 PHE C 339 TYR 0.024 0.001 TYR A 489 ARG 0.011 0.001 ARG C 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7075.41 seconds wall clock time: 126 minutes 48.24 seconds (7608.24 seconds total)