Starting phenix.real_space_refine on Sat Jul 4 02:42:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n17_24115/07_2026/7n17_24115.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n17_24115/07_2026/7n17_24115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n17_24115/07_2026/7n17_24115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n17_24115/07_2026/7n17_24115.map" model { file = "/net/cci-nas-00/data/ceres_data/7n17_24115/07_2026/7n17_24115.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n17_24115/07_2026/7n17_24115.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n17_24115/07_2026/7n17_24115.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n17_24115/07_2026/7n17_24115.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.100 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 96 5.16 5 C 11520 2.51 5 N 2872 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17596 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4270 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain: "B" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4270 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 15, 'TRANS': 501} Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Unusual residues: {'CPL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-3': 6, 'CPL:plan-4': 6, 'CPL:plan-1': 3, 'CPL:plan-2': 3} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Unusual residues: {'CPL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-3': 6, 'CPL:plan-4': 6, 'CPL:plan-1': 3, 'CPL:plan-2': 3} Unresolved non-hydrogen planarities: 68 Restraints were copied for chains: C, D Time building chain proxies: 5.39, per 1000 atoms: 0.31 Number of scatterers: 17596 At special positions: 0 Unit cell: (130.31, 130.31, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 12 15.00 O 3096 8.00 N 2872 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 172 " distance=2.02 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.02 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " distance=2.02 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 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 780.7 milliseconds 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 58.3% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 118 through 145 removed outlier: 3.618A pdb=" N TYR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 224 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.172A pdb=" N ASN A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 286 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 303 through 335 Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 385 through 416 Processing helix chain 'A' and resid 418 through 438 Processing helix chain 'A' and resid 441 through 459 removed outlier: 3.707A pdb=" N LYS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.600A pdb=" N HIS A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 498 through 507 Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 602 through 619 removed outlier: 3.652A pdb=" N ARG A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 118 through 145 removed outlier: 3.617A pdb=" N TYR B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 224 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 276 through 286 removed outlier: 4.172A pdb=" N ASN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 286 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 303 through 335 Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 385 through 416 Processing helix chain 'B' and resid 418 through 438 Processing helix chain 'B' and resid 441 through 459 removed outlier: 3.707A pdb=" N LYS B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.600A pdb=" N HIS B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 498 through 507 Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 602 through 619 removed outlier: 3.652A pdb=" N ARG B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 118 through 145 removed outlier: 3.618A pdb=" N TYR C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 224 Processing helix chain 'C' and resid 236 through 247 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 276 through 286 removed outlier: 4.172A pdb=" N ASN C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 286 " --> pdb=" O ARG C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 303 through 335 Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 385 through 416 Processing helix chain 'C' and resid 418 through 438 Processing helix chain 'C' and resid 441 through 459 removed outlier: 3.707A pdb=" N LYS C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.601A pdb=" N HIS C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 489 Processing helix chain 'C' and resid 498 through 507 Processing helix chain 'C' and resid 592 through 601 Processing helix chain 'C' and resid 602 through 619 removed outlier: 3.652A pdb=" N ARG C 606 " --> pdb=" O TYR C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 118 through 145 removed outlier: 3.618A pdb=" N TYR D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 224 Processing helix chain 'D' and resid 236 through 247 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 265 Processing helix chain 'D' and resid 276 through 286 removed outlier: 4.172A pdb=" N ASN D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 283 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG D 286 " --> pdb=" O ARG D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 303 through 335 Processing helix chain 'D' and resid 358 through 375 Processing helix chain 'D' and resid 385 through 416 Processing helix chain 'D' and resid 418 through 438 Processing helix chain 'D' and resid 441 through 459 removed outlier: 3.707A pdb=" N LYS D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.599A pdb=" N HIS D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 489 Processing helix chain 'D' and resid 498 through 507 Processing helix chain 'D' and resid 592 through 601 Processing helix chain 'D' and resid 602 through 619 removed outlier: 3.652A pdb=" N ARG D 606 " --> pdb=" O TYR D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 171 removed outlier: 3.692A pdb=" N SER A 166 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 161 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 511 through 514 removed outlier: 6.714A pdb=" N ASP A 586 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.659A pdb=" N VAL A 579 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN A 578 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 541 " --> pdb=" O ASN A 578 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 166 through 171 removed outlier: 3.693A pdb=" N SER B 166 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN B 161 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 511 through 514 removed outlier: 6.714A pdb=" N ASP B 586 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 519 through 521 removed outlier: 6.659A pdb=" N VAL B 579 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN B 578 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 541 " --> pdb=" O ASN B 578 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 166 through 171 removed outlier: 3.692A pdb=" N SER C 166 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 161 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 511 through 514 removed outlier: 6.713A pdb=" N ASP C 586 " --> pdb=" O LYS C 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 519 through 521 removed outlier: 6.658A pdb=" N VAL C 579 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN C 578 " --> pdb=" O VAL C 541 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 541 " --> pdb=" O ASN C 578 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 166 through 171 removed outlier: 3.693A pdb=" N SER D 166 " --> pdb=" O ASN D 161 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 161 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 511 through 514 removed outlier: 6.715A pdb=" N ASP D 586 " --> pdb=" O LYS D 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 519 through 521 removed outlier: 6.659A pdb=" N VAL D 579 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN D 578 " --> pdb=" O VAL D 541 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 541 " --> pdb=" O ASN D 578 " (cutoff:3.500A) 969 hydrogen bonds defined for protein. 2811 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: 3.24 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2672 1.30 - 1.43: 5063 1.43 - 1.56: 10069 1.56 - 1.68: 32 1.68 - 1.81: 156 Bond restraints: 17992 Sorted by residual: bond pdb=" C11 CPL C1806 " pdb=" O3 CPL C1806 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C11 CPL A 805 " pdb=" O3 CPL A 805 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C11 CPL B1806 " pdb=" O3 CPL B1806 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 CPL D1801 " pdb=" O2 CPL D1801 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 CPL B1801 " pdb=" O2 CPL B1801 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.28e+01 ... (remaining 17987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 23749 3.86 - 7.71: 479 7.71 - 11.57: 52 11.57 - 15.42: 8 15.42 - 19.28: 12 Bond angle restraints: 24300 Sorted by residual: angle pdb=" O3P CPL C1801 " pdb=" P CPL C1801 " pdb=" O4P CPL C1801 " ideal model delta sigma weight residual 93.29 112.57 -19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O3P CPL B1801 " pdb=" P CPL B1801 " pdb=" O4P CPL B1801 " ideal model delta sigma weight residual 93.29 112.57 -19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O3P CPL D1801 " pdb=" P CPL D1801 " pdb=" O4P CPL D1801 " ideal model delta sigma weight residual 93.29 112.56 -19.27 3.00e+00 1.11e-01 4.13e+01 angle pdb=" O3P CPL A 806 " pdb=" P CPL A 806 " pdb=" O4P CPL A 806 " ideal model delta sigma weight residual 93.29 112.53 -19.24 3.00e+00 1.11e-01 4.11e+01 angle pdb=" O3P CPL C1806 " pdb=" P CPL C1806 " pdb=" O4P CPL C1806 " ideal model delta sigma weight residual 93.29 109.99 -16.70 3.00e+00 1.11e-01 3.10e+01 ... (remaining 24295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9180 17.90 - 35.81: 1160 35.81 - 53.71: 200 53.71 - 71.62: 64 71.62 - 89.52: 32 Dihedral angle restraints: 10636 sinusoidal: 4536 harmonic: 6100 Sorted by residual: dihedral pdb=" CA LYS C 469 " pdb=" C LYS C 469 " pdb=" N VAL C 470 " pdb=" CA VAL C 470 " ideal model delta harmonic sigma weight residual 180.00 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS D 469 " pdb=" C LYS D 469 " pdb=" N VAL D 470 " pdb=" CA VAL D 470 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LYS B 469 " pdb=" C LYS B 469 " pdb=" N VAL B 470 " pdb=" CA VAL B 470 " ideal model delta harmonic sigma weight residual -180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 10633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1926 0.060 - 0.121: 553 0.121 - 0.181: 99 0.181 - 0.241: 54 0.241 - 0.302: 12 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CA PHE A 403 " pdb=" N PHE A 403 " pdb=" C PHE A 403 " pdb=" CB PHE A 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA PHE C 403 " pdb=" N PHE C 403 " pdb=" C PHE C 403 " pdb=" CB PHE C 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PHE D 403 " pdb=" N PHE D 403 " pdb=" C PHE D 403 " pdb=" CB PHE D 403 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2641 not shown) Planarity restraints: 2960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 150 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO C 151 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 150 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO A 151 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 150 " -0.051 5.00e-02 4.00e+02 7.69e-02 9.47e+00 pdb=" N PRO D 151 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 151 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 151 " -0.043 5.00e-02 4.00e+02 ... (remaining 2957 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 6170 2.86 - 3.37: 15520 3.37 - 3.88: 29624 3.88 - 4.39: 33379 4.39 - 4.90: 57961 Nonbonded interactions: 142654 Sorted by model distance: nonbonded pdb=" OH TYR C 112 " pdb=" OE1 GLN C 114 " model vdw 2.355 3.040 nonbonded pdb=" OH TYR A 112 " pdb=" OE1 GLN A 114 " model vdw 2.355 3.040 nonbonded pdb=" OH TYR D 112 " pdb=" OE1 GLN D 114 " model vdw 2.356 3.040 nonbonded pdb=" OH TYR B 112 " pdb=" OE1 GLN B 114 " model vdw 2.356 3.040 nonbonded pdb=" O ASP D 453 " pdb=" OG1 THR D 457 " model vdw 2.368 3.040 ... (remaining 142649 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 103 through 619 or (resid 801 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C2 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C4 or name C5 or name O11 or name O1P or name O2 \ or name O2P or name O3 or name O31 or name O3P or name O4P or name P )) or (resi \ d 802 through 803 and (name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19)) or (resid 804 through 805 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C1 \ 9 or name C20 or name C21 or name C22 or name C23)) or (resid 806 and (name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C2 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name O11 or name O1P or name O2 or name \ O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'B' and (resid 103 through 1801 or (resid 1802 through 1803 and (name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19)) or (resid 1804 through 1805 and (name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or \ name C22 or name C23)) or (resid 1806 and (name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 o \ r name O3P or name O4P or name P )))) selection = (chain 'C' and (resid 103 through 1801 or (resid 1802 through 1803 and (name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19)) or (resid 1804 through 1805 and (name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or \ name C22 or name C23)) or (resid 1806 and (name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 o \ r name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 103 through 1801 or (resid 1802 through 1803 and (name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19)) or (resid 1804 through 1805 and (name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or \ name C22 or name C23)) or (resid 1806 and (name C1 or name C11 or name C12 or na \ me C13 or name C14 or name C2 or name C3 or name C31 or name C32 or name C33 or \ name C34 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 o \ r name O3P or name O4P or name P )))) } 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.660 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 : 0.009 0.103 17996 Z= 0.407 Angle : 1.325 19.278 24308 Z= 0.649 Chirality : 0.065 0.302 2644 Planarity : 0.009 0.077 2960 Dihedral : 16.643 89.521 6712 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.28 % Allowed : 6.62 % Favored : 92.09 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.12), residues: 2060 helix: -3.59 (0.08), residues: 1204 sheet: -1.96 (0.32), residues: 192 loop : -1.70 (0.18), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 614 TYR 0.029 0.003 TYR D 363 PHE 0.019 0.003 PHE D 328 TRP 0.027 0.003 TRP D 266 HIS 0.006 0.002 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.41 (17992) covalent geometry : angle 1.32481 / 0.65 (24300) SS BOND : bond 0.00880 / 0.42 ( 4) SS BOND : angle 1.06060 / 0.58 ( 8) hydrogen bonds : bond 0.17260 / 11.43 ( 969) hydrogen bonds : angle 7.42289 / 5.13 ( 2811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 112 TYR cc_start: 0.8466 (t80) cc_final: 0.7996 (t80) REVERT: A 270 TYR cc_start: 0.7490 (m-80) cc_final: 0.7161 (m-80) REVERT: A 397 MET cc_start: 0.7596 (mmm) cc_final: 0.7249 (mtm) REVERT: A 426 ASN cc_start: 0.8321 (m110) cc_final: 0.7894 (m110) REVERT: A 478 GLU cc_start: 0.8256 (tp30) cc_final: 0.7925 (tp30) REVERT: A 537 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7636 (ttm110) REVERT: B 112 TYR cc_start: 0.8455 (t80) cc_final: 0.7934 (t80) REVERT: B 270 TYR cc_start: 0.7479 (m-80) cc_final: 0.7159 (m-80) REVERT: B 397 MET cc_start: 0.7596 (mmm) cc_final: 0.7214 (mtm) REVERT: B 426 ASN cc_start: 0.8310 (m110) cc_final: 0.7934 (m110) REVERT: B 478 GLU cc_start: 0.8233 (tp30) cc_final: 0.7889 (tp30) REVERT: B 537 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7264 (ttm110) REVERT: C 112 TYR cc_start: 0.8454 (t80) cc_final: 0.7957 (t80) REVERT: C 270 TYR cc_start: 0.7506 (m-80) cc_final: 0.7180 (m-80) REVERT: C 397 MET cc_start: 0.7598 (mmm) cc_final: 0.7238 (mtm) REVERT: C 426 ASN cc_start: 0.8259 (m110) cc_final: 0.7884 (m110) REVERT: C 478 GLU cc_start: 0.8212 (tp30) cc_final: 0.7873 (tp30) REVERT: C 537 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7274 (ttm110) REVERT: D 270 TYR cc_start: 0.7511 (m-80) cc_final: 0.7182 (m-80) REVERT: D 397 MET cc_start: 0.7554 (mmm) cc_final: 0.7207 (mtm) REVERT: D 426 ASN cc_start: 0.8324 (m110) cc_final: 0.7917 (m110) REVERT: D 478 GLU cc_start: 0.8232 (tp30) cc_final: 0.7905 (tp30) REVERT: D 537 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7606 (ttm110) REVERT: D 558 PHE cc_start: 0.8292 (p90) cc_final: 0.7988 (p90) outliers start: 24 outliers final: 4 residues processed: 316 average time/residue: 0.1508 time to fit residues: 70.9214 Evaluate side-chains 221 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0670 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 GLN A 578 ASN B 426 ASN B 482 GLN B 578 ASN C 426 ASN C 578 ASN D 246 GLN D 425 GLN D 482 GLN D 578 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.175643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130429 restraints weight = 20154.656| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.08 r_work: 0.3095 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17996 Z= 0.115 Angle : 0.534 7.081 24308 Z= 0.281 Chirality : 0.040 0.153 2644 Planarity : 0.005 0.038 2960 Dihedral : 10.483 63.008 2624 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.43 % Allowed : 8.97 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.16), residues: 2060 helix: -0.65 (0.13), residues: 1188 sheet: -0.77 (0.36), residues: 184 loop : -1.01 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 280 TYR 0.011 0.001 TYR D 363 PHE 0.018 0.001 PHE B 558 TRP 0.015 0.001 TRP C 329 HIS 0.001 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (17992) covalent geometry : angle 0.53354 / 0.28 (24300) SS BOND : bond 0.00032 / 0.01 ( 4) SS BOND : angle 0.82484 / 0.45 ( 8) hydrogen bonds : bond 0.04193 / 2.72 ( 969) hydrogen bonds : angle 4.67099 / 3.21 ( 2811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 0.681 Fit side-chains REVERT: A 262 TYR cc_start: 0.8817 (m-80) cc_final: 0.8521 (m-80) REVERT: A 270 TYR cc_start: 0.7962 (m-80) cc_final: 0.7677 (m-80) REVERT: A 426 ASN cc_start: 0.8195 (m110) cc_final: 0.7758 (m110) REVERT: A 478 GLU cc_start: 0.8136 (tp30) cc_final: 0.7782 (tp30) REVERT: A 481 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8015 (mmm) REVERT: A 537 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7876 (ttm110) REVERT: A 588 PHE cc_start: 0.8537 (m-80) cc_final: 0.8245 (m-10) REVERT: B 262 TYR cc_start: 0.8804 (m-80) cc_final: 0.8522 (m-80) REVERT: B 270 TYR cc_start: 0.7954 (m-80) cc_final: 0.7682 (m-80) REVERT: B 426 ASN cc_start: 0.8192 (m-40) cc_final: 0.7758 (m110) REVERT: B 478 GLU cc_start: 0.8210 (tp30) cc_final: 0.7885 (tp30) REVERT: B 485 PHE cc_start: 0.8239 (t80) cc_final: 0.7841 (t80) REVERT: B 510 GLN cc_start: 0.8026 (pt0) cc_final: 0.7728 (mt0) REVERT: B 537 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7880 (ttm110) REVERT: B 588 PHE cc_start: 0.8486 (m-80) cc_final: 0.8248 (m-10) REVERT: C 262 TYR cc_start: 0.8807 (m-80) cc_final: 0.8526 (m-80) REVERT: C 270 TYR cc_start: 0.7950 (m-80) cc_final: 0.7682 (m-80) REVERT: C 426 ASN cc_start: 0.8082 (m-40) cc_final: 0.7664 (m110) REVERT: C 478 GLU cc_start: 0.8165 (tp30) cc_final: 0.7814 (tp30) REVERT: C 529 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7469 (mt-10) REVERT: C 535 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7455 (ttp80) REVERT: C 537 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7919 (ttm110) REVERT: C 588 PHE cc_start: 0.8460 (m-80) cc_final: 0.8100 (m-10) REVERT: D 270 TYR cc_start: 0.7965 (m-80) cc_final: 0.7677 (m-80) REVERT: D 426 ASN cc_start: 0.8282 (m110) cc_final: 0.7863 (m110) REVERT: D 478 GLU cc_start: 0.8197 (tp30) cc_final: 0.7833 (tp30) REVERT: D 537 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7866 (ttm110) outliers start: 8 outliers final: 3 residues processed: 263 average time/residue: 0.1399 time to fit residues: 56.7077 Evaluate side-chains 220 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 216 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain D residue 382 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 159 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN B 482 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 ASN D 482 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.171863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110706 restraints weight = 20391.665| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.93 r_work: 0.3113 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17996 Z= 0.192 Angle : 0.558 7.564 24308 Z= 0.288 Chirality : 0.043 0.157 2644 Planarity : 0.004 0.035 2960 Dihedral : 9.773 59.963 2620 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.28 % Allowed : 11.22 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2060 helix: 0.39 (0.15), residues: 1184 sheet: -0.19 (0.38), residues: 160 loop : -0.72 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 537 TYR 0.016 0.001 TYR B 363 PHE 0.023 0.002 PHE C 558 TRP 0.013 0.001 TRP D 329 HIS 0.002 0.001 HIS C 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (17992) covalent geometry : angle 0.55759 / 0.29 (24300) SS BOND : bond 0.00025 / 0.01 ( 4) SS BOND : angle 0.75638 / 0.42 ( 8) hydrogen bonds : bond 0.04253 / 2.74 ( 969) hydrogen bonds : angle 4.37163 / 3.01 ( 2811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.8793 (m-80) cc_final: 0.8569 (m-80) REVERT: A 270 TYR cc_start: 0.8061 (m-80) cc_final: 0.7759 (m-80) REVERT: A 426 ASN cc_start: 0.8235 (m-40) cc_final: 0.7823 (m110) REVERT: A 436 GLU cc_start: 0.8047 (tp30) cc_final: 0.7762 (tp30) REVERT: A 478 GLU cc_start: 0.8211 (tp30) cc_final: 0.7815 (tp30) REVERT: A 481 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8068 (mmm) REVERT: A 537 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.7901 (ttm110) REVERT: A 588 PHE cc_start: 0.8605 (m-80) cc_final: 0.8297 (m-10) REVERT: B 262 TYR cc_start: 0.8788 (m-80) cc_final: 0.8568 (m-80) REVERT: B 270 TYR cc_start: 0.8027 (m-80) cc_final: 0.7735 (m-80) REVERT: B 426 ASN cc_start: 0.8273 (m-40) cc_final: 0.7839 (m110) REVERT: B 436 GLU cc_start: 0.8059 (tp30) cc_final: 0.7831 (tp30) REVERT: B 453 ASP cc_start: 0.7677 (m-30) cc_final: 0.7204 (m-30) REVERT: B 478 GLU cc_start: 0.8257 (tp30) cc_final: 0.7887 (tp30) REVERT: B 537 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7917 (ttm110) REVERT: B 588 PHE cc_start: 0.8588 (m-80) cc_final: 0.8375 (m-10) REVERT: C 262 TYR cc_start: 0.8779 (m-80) cc_final: 0.8562 (m-80) REVERT: C 270 TYR cc_start: 0.8044 (m-80) cc_final: 0.7743 (m-80) REVERT: C 426 ASN cc_start: 0.8237 (m-40) cc_final: 0.7811 (m110) REVERT: C 478 GLU cc_start: 0.8178 (tp30) cc_final: 0.7957 (tp30) REVERT: C 481 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: C 535 ARG cc_start: 0.8254 (ttp-110) cc_final: 0.7516 (ttp80) REVERT: C 537 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7924 (ttm110) REVERT: C 588 PHE cc_start: 0.8579 (m-80) cc_final: 0.8261 (m-10) REVERT: D 262 TYR cc_start: 0.8901 (m-80) cc_final: 0.8645 (m-80) REVERT: D 270 TYR cc_start: 0.8064 (m-80) cc_final: 0.7758 (m-80) REVERT: D 426 ASN cc_start: 0.8352 (m-40) cc_final: 0.7939 (m110) REVERT: D 478 GLU cc_start: 0.8253 (tp30) cc_final: 0.7887 (tp30) REVERT: D 535 ARG cc_start: 0.8273 (ttp-110) cc_final: 0.7567 (ttp80) outliers start: 24 outliers final: 11 residues processed: 234 average time/residue: 0.1436 time to fit residues: 50.9751 Evaluate side-chains 216 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 382 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 195 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS A 460 GLN B 199 HIS B 460 GLN C 199 HIS C 460 GLN D 460 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113872 restraints weight = 20406.405| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.94 r_work: 0.3175 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17996 Z= 0.112 Angle : 0.490 7.375 24308 Z= 0.252 Chirality : 0.040 0.144 2644 Planarity : 0.003 0.038 2960 Dihedral : 8.771 61.476 2620 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.75 % Allowed : 12.07 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2060 helix: 0.88 (0.15), residues: 1208 sheet: 0.11 (0.36), residues: 160 loop : -0.48 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 280 TYR 0.011 0.001 TYR B 363 PHE 0.016 0.001 PHE C 558 TRP 0.011 0.001 TRP D 329 HIS 0.001 0.000 HIS C 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (17992) covalent geometry : angle 0.48945 / 0.25 (24300) SS BOND : bond 0.00120 / 0.06 ( 4) SS BOND : angle 0.70851 / 0.39 ( 8) hydrogen bonds : bond 0.03667 / 2.36 ( 969) hydrogen bonds : angle 4.07310 / 2.81 ( 2811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.729 Fit side-chains REVERT: A 191 ASP cc_start: 0.9002 (p0) cc_final: 0.8790 (p0) REVERT: A 270 TYR cc_start: 0.8046 (m-80) cc_final: 0.7773 (m-80) REVERT: A 423 GLU cc_start: 0.8406 (tp30) cc_final: 0.8144 (tp30) REVERT: A 426 ASN cc_start: 0.8179 (m-40) cc_final: 0.7754 (m110) REVERT: A 436 GLU cc_start: 0.8017 (tp30) cc_final: 0.7704 (tp30) REVERT: A 478 GLU cc_start: 0.8179 (tp30) cc_final: 0.7783 (tp30) REVERT: A 481 MET cc_start: 0.8411 (mmt) cc_final: 0.8070 (mmm) REVERT: A 537 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.7973 (ttm110) REVERT: B 191 ASP cc_start: 0.8984 (p0) cc_final: 0.8781 (p0) REVERT: B 270 TYR cc_start: 0.8003 (m-80) cc_final: 0.7707 (t80) REVERT: B 426 ASN cc_start: 0.8217 (m-40) cc_final: 0.7786 (m110) REVERT: B 436 GLU cc_start: 0.7974 (tp30) cc_final: 0.7695 (tp30) REVERT: B 453 ASP cc_start: 0.7614 (m-30) cc_final: 0.7097 (m-30) REVERT: B 478 GLU cc_start: 0.8217 (tp30) cc_final: 0.7829 (tp30) REVERT: B 481 MET cc_start: 0.8444 (mmt) cc_final: 0.8093 (mmm) REVERT: B 535 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7534 (ttp80) REVERT: B 537 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7936 (ttm110) REVERT: B 554 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8170 (tm-30) REVERT: C 191 ASP cc_start: 0.9001 (p0) cc_final: 0.8786 (p0) REVERT: C 270 TYR cc_start: 0.8007 (m-80) cc_final: 0.7729 (m-80) REVERT: C 416 ASN cc_start: 0.8820 (t0) cc_final: 0.8610 (t0) REVERT: C 423 GLU cc_start: 0.8394 (tp30) cc_final: 0.8109 (tp30) REVERT: C 426 ASN cc_start: 0.8169 (m-40) cc_final: 0.7742 (m110) REVERT: C 438 ARG cc_start: 0.7571 (mpt180) cc_final: 0.7223 (mpt180) REVERT: C 453 ASP cc_start: 0.7632 (m-30) cc_final: 0.7093 (m-30) REVERT: C 478 GLU cc_start: 0.8189 (tp30) cc_final: 0.7955 (tp30) REVERT: C 481 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8071 (mmm) REVERT: C 537 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.7965 (ttm110) REVERT: C 554 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8182 (tm-30) REVERT: C 588 PHE cc_start: 0.8552 (m-80) cc_final: 0.8235 (m-10) REVERT: D 191 ASP cc_start: 0.8997 (p0) cc_final: 0.8774 (p0) REVERT: D 270 TYR cc_start: 0.8009 (m-80) cc_final: 0.7732 (m-80) REVERT: D 423 GLU cc_start: 0.8465 (tp30) cc_final: 0.8200 (tp30) REVERT: D 426 ASN cc_start: 0.8270 (m-40) cc_final: 0.7833 (m110) REVERT: D 478 GLU cc_start: 0.8208 (tp30) cc_final: 0.7826 (tp30) REVERT: D 481 MET cc_start: 0.8401 (mmt) cc_final: 0.8050 (mmm) REVERT: D 485 PHE cc_start: 0.8106 (t80) cc_final: 0.7740 (t80) REVERT: D 535 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7635 (ttp80) REVERT: D 537 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7885 (ttm110) outliers start: 14 outliers final: 5 residues processed: 245 average time/residue: 0.1418 time to fit residues: 52.8136 Evaluate side-chains 214 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain D residue 382 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 153 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.126091 restraints weight = 20331.687| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.67 r_work: 0.2981 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 17996 Z= 0.233 Angle : 0.574 8.238 24308 Z= 0.296 Chirality : 0.043 0.154 2644 Planarity : 0.004 0.036 2960 Dihedral : 9.150 57.576 2620 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.60 % Allowed : 11.49 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2060 helix: 0.79 (0.15), residues: 1208 sheet: -0.08 (0.36), residues: 168 loop : -0.49 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 580 TYR 0.016 0.001 TYR B 363 PHE 0.017 0.002 PHE C 328 TRP 0.012 0.001 TRP D 596 HIS 0.004 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (17992) covalent geometry : angle 0.57388 / 0.30 (24300) SS BOND : bond 0.00017 / 0.01 ( 4) SS BOND : angle 0.71853 / 0.39 ( 8) hydrogen bonds : bond 0.04318 / 2.79 ( 969) hydrogen bonds : angle 4.20330 / 2.90 ( 2811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.8863 (m-80) cc_final: 0.8611 (m-80) REVERT: A 270 TYR cc_start: 0.8023 (m-80) cc_final: 0.7754 (m-80) REVERT: A 423 GLU cc_start: 0.8451 (tp30) cc_final: 0.8202 (tp30) REVERT: A 426 ASN cc_start: 0.8351 (m-40) cc_final: 0.7924 (m110) REVERT: A 436 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: A 478 GLU cc_start: 0.8214 (tp30) cc_final: 0.7823 (tp30) REVERT: A 481 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8043 (mmm) REVERT: A 535 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8086 (ttp80) REVERT: A 537 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.7824 (ttm110) REVERT: B 262 TYR cc_start: 0.8861 (m-80) cc_final: 0.8612 (m-80) REVERT: B 270 TYR cc_start: 0.8021 (m-80) cc_final: 0.7728 (m-80) REVERT: B 423 GLU cc_start: 0.8439 (tp30) cc_final: 0.8185 (tp30) REVERT: B 426 ASN cc_start: 0.8323 (m-40) cc_final: 0.7885 (m110) REVERT: B 436 GLU cc_start: 0.8017 (tp30) cc_final: 0.7691 (tp30) REVERT: B 478 GLU cc_start: 0.8271 (tp30) cc_final: 0.7894 (tp30) REVERT: B 535 ARG cc_start: 0.8275 (ttp-110) cc_final: 0.7951 (ttp80) REVERT: B 537 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.7823 (ttm110) REVERT: C 262 TYR cc_start: 0.8860 (m-80) cc_final: 0.8616 (m-80) REVERT: C 270 TYR cc_start: 0.7992 (m-80) cc_final: 0.7714 (m-80) REVERT: C 426 ASN cc_start: 0.8304 (m-40) cc_final: 0.7866 (m110) REVERT: C 478 GLU cc_start: 0.8245 (tp30) cc_final: 0.7831 (tp30) REVERT: C 481 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8099 (mmm) REVERT: C 535 ARG cc_start: 0.8248 (ttp80) cc_final: 0.8019 (ttp80) REVERT: C 537 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.7800 (ttm110) REVERT: C 588 PHE cc_start: 0.8581 (m-80) cc_final: 0.8260 (m-10) REVERT: C 589 VAL cc_start: 0.8919 (t) cc_final: 0.8711 (m) REVERT: D 270 TYR cc_start: 0.8008 (m-80) cc_final: 0.7727 (m-80) REVERT: D 423 GLU cc_start: 0.8469 (tp30) cc_final: 0.8231 (tp30) REVERT: D 426 ASN cc_start: 0.8373 (m-40) cc_final: 0.7949 (m110) REVERT: D 437 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7900 (mp) REVERT: D 478 GLU cc_start: 0.8238 (tp30) cc_final: 0.7850 (tp30) REVERT: D 535 ARG cc_start: 0.8306 (ttp-110) cc_final: 0.7598 (ttp80) REVERT: D 537 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7846 (ttm110) outliers start: 30 outliers final: 19 residues processed: 230 average time/residue: 0.1273 time to fit residues: 45.3527 Evaluate side-chains 229 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 108 optimal weight: 6.9990 chunk 41 optimal weight: 0.0970 chunk 126 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 HIS D 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128919 restraints weight = 20222.328| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.25 r_work: 0.3061 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17996 Z= 0.107 Angle : 0.482 7.167 24308 Z= 0.250 Chirality : 0.040 0.138 2644 Planarity : 0.003 0.039 2960 Dihedral : 8.177 58.901 2620 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.80 % Allowed : 13.19 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 2060 helix: 1.15 (0.15), residues: 1212 sheet: 0.48 (0.37), residues: 160 loop : -0.38 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 580 TYR 0.011 0.001 TYR B 365 PHE 0.012 0.001 PHE C 328 TRP 0.011 0.001 TRP C 124 HIS 0.001 0.000 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (17992) covalent geometry : angle 0.48142 / 0.25 (24300) SS BOND : bond 0.00090 / 0.04 ( 4) SS BOND : angle 0.68770 / 0.37 ( 8) hydrogen bonds : bond 0.03522 / 2.27 ( 969) hydrogen bonds : angle 3.94262 / 2.72 ( 2811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.8758 (m-80) cc_final: 0.8486 (m-80) REVERT: A 270 TYR cc_start: 0.7957 (m-80) cc_final: 0.7668 (t80) REVERT: A 423 GLU cc_start: 0.8430 (tp30) cc_final: 0.8171 (tp30) REVERT: A 426 ASN cc_start: 0.8134 (m-40) cc_final: 0.7698 (m110) REVERT: A 436 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: A 478 GLU cc_start: 0.8130 (tp30) cc_final: 0.7736 (tp30) REVERT: A 481 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8045 (mmm) REVERT: A 535 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7786 (ttp80) REVERT: A 537 ARG cc_start: 0.8242 (ttm-80) cc_final: 0.7828 (ttm110) REVERT: A 586 ASP cc_start: 0.8593 (m-30) cc_final: 0.8360 (m-30) REVERT: B 262 TYR cc_start: 0.8740 (m-80) cc_final: 0.8471 (m-80) REVERT: B 270 TYR cc_start: 0.7941 (m-80) cc_final: 0.7647 (t80) REVERT: B 423 GLU cc_start: 0.8410 (tp30) cc_final: 0.8151 (tp30) REVERT: B 426 ASN cc_start: 0.8134 (m-40) cc_final: 0.7704 (m110) REVERT: B 436 GLU cc_start: 0.7909 (tp30) cc_final: 0.7618 (tp30) REVERT: B 478 GLU cc_start: 0.8202 (tp30) cc_final: 0.7828 (tp30) REVERT: B 508 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8450 (mmtp) REVERT: B 535 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.7413 (ttp80) REVERT: B 537 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7775 (ttm110) REVERT: C 262 TYR cc_start: 0.8740 (m-80) cc_final: 0.8472 (m-80) REVERT: C 423 GLU cc_start: 0.8400 (tp30) cc_final: 0.8112 (tp30) REVERT: C 426 ASN cc_start: 0.8109 (m-40) cc_final: 0.7684 (m110) REVERT: C 436 GLU cc_start: 0.7928 (tp30) cc_final: 0.7686 (tp30) REVERT: C 438 ARG cc_start: 0.7507 (mpt180) cc_final: 0.7029 (mpt180) REVERT: C 478 GLU cc_start: 0.8189 (tp30) cc_final: 0.7757 (tp30) REVERT: C 481 MET cc_start: 0.8381 (mmt) cc_final: 0.8059 (mmm) REVERT: C 535 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7935 (ttp80) REVERT: C 537 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7792 (ttm110) REVERT: C 588 PHE cc_start: 0.8535 (m-80) cc_final: 0.8290 (m-10) REVERT: D 270 TYR cc_start: 0.7966 (m-80) cc_final: 0.7685 (t80) REVERT: D 423 GLU cc_start: 0.8447 (tp30) cc_final: 0.8188 (tp30) REVERT: D 426 ASN cc_start: 0.8171 (m-40) cc_final: 0.7736 (m110) REVERT: D 478 GLU cc_start: 0.8177 (tp30) cc_final: 0.7779 (tp30) REVERT: D 485 PHE cc_start: 0.8083 (t80) cc_final: 0.7724 (t80) REVERT: D 535 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7620 (ttp80) REVERT: D 537 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7855 (ttm110) outliers start: 15 outliers final: 8 residues processed: 228 average time/residue: 0.1319 time to fit residues: 45.7051 Evaluate side-chains 219 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 20 optimal weight: 0.7980 chunk 146 optimal weight: 0.0370 chunk 111 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.173087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112751 restraints weight = 20279.948| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.87 r_work: 0.3155 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17996 Z= 0.129 Angle : 0.501 7.001 24308 Z= 0.259 Chirality : 0.040 0.156 2644 Planarity : 0.003 0.037 2960 Dihedral : 8.033 56.852 2620 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.85 % Allowed : 13.51 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 2060 helix: 1.22 (0.15), residues: 1212 sheet: 0.52 (0.43), residues: 120 loop : -0.32 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 580 TYR 0.010 0.001 TYR C 365 PHE 0.013 0.001 PHE A 328 TRP 0.009 0.001 TRP A 456 HIS 0.002 0.001 HIS D 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17992) covalent geometry : angle 0.50046 / 0.26 (24300) SS BOND : bond 0.00078 / 0.04 ( 4) SS BOND : angle 0.69204 / 0.38 ( 8) hydrogen bonds : bond 0.03663 / 2.36 ( 969) hydrogen bonds : angle 3.90480 / 2.70 ( 2811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.831 Fit side-chains REVERT: A 270 TYR cc_start: 0.8032 (m-80) cc_final: 0.7678 (t80) REVERT: A 423 GLU cc_start: 0.8480 (tp30) cc_final: 0.8222 (tp30) REVERT: A 426 ASN cc_start: 0.8286 (m-40) cc_final: 0.7884 (m110) REVERT: A 436 GLU cc_start: 0.7968 (tp30) cc_final: 0.7643 (tp30) REVERT: A 478 GLU cc_start: 0.8159 (tp30) cc_final: 0.7769 (tp30) REVERT: A 481 MET cc_start: 0.8369 (mmt) cc_final: 0.8045 (mmm) REVERT: A 535 ARG cc_start: 0.8358 (ttp80) cc_final: 0.7963 (ttp80) REVERT: A 537 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7819 (ttm110) REVERT: B 262 TYR cc_start: 0.8742 (m-80) cc_final: 0.8539 (m-80) REVERT: B 270 TYR cc_start: 0.7999 (m-80) cc_final: 0.7684 (t80) REVERT: B 423 GLU cc_start: 0.8477 (tp30) cc_final: 0.8215 (tp30) REVERT: B 426 ASN cc_start: 0.8251 (m-40) cc_final: 0.7866 (m110) REVERT: B 436 GLU cc_start: 0.7948 (tp30) cc_final: 0.7661 (tp30) REVERT: B 478 GLU cc_start: 0.8189 (tp30) cc_final: 0.7818 (tp30) REVERT: B 535 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.7454 (ttp80) REVERT: B 537 ARG cc_start: 0.8300 (ttm-80) cc_final: 0.7841 (ttm110) REVERT: C 262 TYR cc_start: 0.8748 (m-80) cc_final: 0.8547 (m-80) REVERT: C 423 GLU cc_start: 0.8501 (tp30) cc_final: 0.8231 (tp30) REVERT: C 426 ASN cc_start: 0.8187 (m-40) cc_final: 0.7763 (m110) REVERT: C 478 GLU cc_start: 0.8211 (tp30) cc_final: 0.7788 (tp30) REVERT: C 481 MET cc_start: 0.8399 (mmt) cc_final: 0.8074 (mmm) REVERT: C 535 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7885 (ttp80) REVERT: C 537 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7875 (ttm110) REVERT: C 588 PHE cc_start: 0.8505 (m-80) cc_final: 0.8230 (m-10) REVERT: D 270 TYR cc_start: 0.8022 (m-80) cc_final: 0.7746 (t80) REVERT: D 423 GLU cc_start: 0.8508 (tp30) cc_final: 0.8237 (tp30) REVERT: D 426 ASN cc_start: 0.8289 (m-40) cc_final: 0.7849 (m110) REVERT: D 478 GLU cc_start: 0.8189 (tp30) cc_final: 0.7795 (tp30) REVERT: D 481 MET cc_start: 0.8437 (mmt) cc_final: 0.8080 (mmm) REVERT: D 535 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.7984 (ttp80) REVERT: D 537 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.7904 (ttm110) outliers start: 16 outliers final: 10 residues processed: 219 average time/residue: 0.1404 time to fit residues: 46.5763 Evaluate side-chains 212 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 58 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115955 restraints weight = 20275.575| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.13 r_work: 0.3119 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17996 Z= 0.126 Angle : 0.502 8.717 24308 Z= 0.258 Chirality : 0.040 0.163 2644 Planarity : 0.003 0.038 2960 Dihedral : 7.871 55.323 2620 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.75 % Allowed : 13.57 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 2060 helix: 1.28 (0.15), residues: 1212 sheet: 0.57 (0.44), residues: 120 loop : -0.29 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 580 TYR 0.010 0.001 TYR D 363 PHE 0.013 0.001 PHE C 328 TRP 0.010 0.001 TRP A 456 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (17992) covalent geometry : angle 0.50233 / 0.26 (24300) SS BOND : bond 0.00065 / 0.03 ( 4) SS BOND : angle 0.69886 / 0.38 ( 8) hydrogen bonds : bond 0.03631 / 2.34 ( 969) hydrogen bonds : angle 3.88153 / 2.69 ( 2811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.641 Fit side-chains REVERT: A 270 TYR cc_start: 0.8098 (m-80) cc_final: 0.7717 (t80) REVERT: A 423 GLU cc_start: 0.8539 (tp30) cc_final: 0.8283 (tp30) REVERT: A 426 ASN cc_start: 0.8344 (m-40) cc_final: 0.7943 (m110) REVERT: A 436 GLU cc_start: 0.8026 (tp30) cc_final: 0.7716 (tp30) REVERT: A 478 GLU cc_start: 0.8140 (tp30) cc_final: 0.7752 (tp30) REVERT: A 481 MET cc_start: 0.8375 (mmt) cc_final: 0.8067 (mmm) REVERT: A 537 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.7892 (ttm110) REVERT: A 586 ASP cc_start: 0.8689 (m-30) cc_final: 0.8326 (m-30) REVERT: B 262 TYR cc_start: 0.8714 (m-80) cc_final: 0.8433 (m-80) REVERT: B 270 TYR cc_start: 0.8074 (m-80) cc_final: 0.7726 (t80) REVERT: B 423 GLU cc_start: 0.8526 (tp30) cc_final: 0.8263 (tp30) REVERT: B 426 ASN cc_start: 0.8299 (m-40) cc_final: 0.7916 (m110) REVERT: B 436 GLU cc_start: 0.7992 (tp30) cc_final: 0.7717 (tp30) REVERT: B 438 ARG cc_start: 0.7721 (mpt180) cc_final: 0.7399 (mpt180) REVERT: B 478 GLU cc_start: 0.8196 (tp30) cc_final: 0.7831 (tp30) REVERT: B 535 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.8019 (ttp80) REVERT: B 537 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.7916 (ttm110) REVERT: C 262 TYR cc_start: 0.8708 (m-80) cc_final: 0.8436 (m-80) REVERT: C 423 GLU cc_start: 0.8568 (tp30) cc_final: 0.8303 (tp30) REVERT: C 426 ASN cc_start: 0.8234 (m-40) cc_final: 0.7810 (m110) REVERT: C 436 GLU cc_start: 0.8008 (tp30) cc_final: 0.7790 (tp30) REVERT: C 478 GLU cc_start: 0.8228 (tp30) cc_final: 0.7809 (tp30) REVERT: C 481 MET cc_start: 0.8398 (mmt) cc_final: 0.8078 (mmm) REVERT: C 535 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7951 (ttp80) REVERT: C 537 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.7911 (ttm110) REVERT: C 588 PHE cc_start: 0.8539 (m-80) cc_final: 0.8293 (m-10) REVERT: D 270 TYR cc_start: 0.8096 (m-80) cc_final: 0.7736 (t80) REVERT: D 423 GLU cc_start: 0.8567 (tp30) cc_final: 0.8302 (tp30) REVERT: D 426 ASN cc_start: 0.8337 (m-40) cc_final: 0.7948 (m110) REVERT: D 478 GLU cc_start: 0.8213 (tp30) cc_final: 0.7824 (tp30) REVERT: D 481 MET cc_start: 0.8431 (mmt) cc_final: 0.8072 (mmm) REVERT: D 535 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.7887 (ttp80) REVERT: D 537 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7893 (ttm110) REVERT: D 586 ASP cc_start: 0.8764 (m-30) cc_final: 0.8485 (m-30) outliers start: 14 outliers final: 12 residues processed: 218 average time/residue: 0.1455 time to fit residues: 47.8262 Evaluate side-chains 220 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 56 optimal weight: 8.9990 chunk 192 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 150 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.173811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118769 restraints weight = 20505.582| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.85 r_work: 0.3187 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17996 Z= 0.148 Angle : 0.522 9.064 24308 Z= 0.266 Chirality : 0.041 0.168 2644 Planarity : 0.003 0.038 2960 Dihedral : 7.996 54.211 2620 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.07 % Allowed : 13.51 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 2060 helix: 1.25 (0.15), residues: 1212 sheet: 0.56 (0.45), residues: 120 loop : -0.29 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 580 TYR 0.011 0.001 TYR D 363 PHE 0.014 0.001 PHE A 328 TRP 0.010 0.001 TRP A 456 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (17992) covalent geometry : angle 0.52230 / 0.27 (24300) SS BOND : bond 0.00037 / 0.02 ( 4) SS BOND : angle 0.71293 / 0.39 ( 8) hydrogen bonds : bond 0.03777 / 2.43 ( 969) hydrogen bonds : angle 3.92143 / 2.72 ( 2811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.704 Fit side-chains REVERT: A 270 TYR cc_start: 0.8019 (m-80) cc_final: 0.7645 (t80) REVERT: A 423 GLU cc_start: 0.8528 (tp30) cc_final: 0.8263 (tp30) REVERT: A 426 ASN cc_start: 0.8348 (m-40) cc_final: 0.7935 (m110) REVERT: A 436 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: A 478 GLU cc_start: 0.8147 (tp30) cc_final: 0.7729 (tp30) REVERT: A 481 MET cc_start: 0.8369 (mmt) cc_final: 0.8048 (mmm) REVERT: A 537 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7706 (ttm110) REVERT: A 586 ASP cc_start: 0.8648 (m-30) cc_final: 0.8211 (m-30) REVERT: B 262 TYR cc_start: 0.8691 (m-80) cc_final: 0.8447 (m-80) REVERT: B 270 TYR cc_start: 0.8016 (m-80) cc_final: 0.7667 (t80) REVERT: B 423 GLU cc_start: 0.8533 (tp30) cc_final: 0.8244 (tp30) REVERT: B 426 ASN cc_start: 0.8261 (m-40) cc_final: 0.7842 (m110) REVERT: B 436 GLU cc_start: 0.7930 (tp30) cc_final: 0.7643 (tp30) REVERT: B 438 ARG cc_start: 0.7633 (mpt180) cc_final: 0.7223 (mpt180) REVERT: B 478 GLU cc_start: 0.8149 (tp30) cc_final: 0.7774 (tp30) REVERT: B 535 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7873 (ttp80) REVERT: B 537 ARG cc_start: 0.8267 (ttm-80) cc_final: 0.7743 (ttm110) REVERT: C 262 TYR cc_start: 0.8704 (m-80) cc_final: 0.8458 (m-80) REVERT: C 423 GLU cc_start: 0.8549 (tp30) cc_final: 0.8256 (tp30) REVERT: C 426 ASN cc_start: 0.8181 (m-40) cc_final: 0.7786 (m110) REVERT: C 436 GLU cc_start: 0.7992 (tp30) cc_final: 0.7776 (tp30) REVERT: C 478 GLU cc_start: 0.8211 (tp30) cc_final: 0.7780 (tp30) REVERT: C 481 MET cc_start: 0.8391 (mmt) cc_final: 0.8069 (mmm) REVERT: C 537 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7702 (ttm110) REVERT: C 586 ASP cc_start: 0.8627 (m-30) cc_final: 0.8165 (m-30) REVERT: C 588 PHE cc_start: 0.8465 (m-80) cc_final: 0.8196 (m-10) REVERT: D 270 TYR cc_start: 0.8054 (m-80) cc_final: 0.7708 (t80) REVERT: D 423 GLU cc_start: 0.8549 (tp30) cc_final: 0.8265 (tp30) REVERT: D 426 ASN cc_start: 0.8302 (m-40) cc_final: 0.7900 (m110) REVERT: D 478 GLU cc_start: 0.8199 (tp30) cc_final: 0.7789 (tp30) REVERT: D 481 MET cc_start: 0.8414 (mmt) cc_final: 0.8061 (mmm) REVERT: D 535 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.7736 (ttp80) REVERT: D 537 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.7805 (ttm110) REVERT: D 586 ASP cc_start: 0.8741 (m-30) cc_final: 0.8429 (m-30) outliers start: 20 outliers final: 18 residues processed: 222 average time/residue: 0.1446 time to fit residues: 48.9159 Evaluate side-chains 222 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 29 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.173849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117034 restraints weight = 20501.363| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.06 r_work: 0.3154 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17996 Z= 0.135 Angle : 0.514 9.082 24308 Z= 0.262 Chirality : 0.041 0.166 2644 Planarity : 0.003 0.038 2960 Dihedral : 7.937 59.687 2620 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.01 % Allowed : 13.46 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 2060 helix: 1.29 (0.15), residues: 1212 sheet: 0.63 (0.46), residues: 120 loop : -0.22 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 580 TYR 0.010 0.001 TYR A 363 PHE 0.013 0.001 PHE D 328 TRP 0.010 0.001 TRP B 456 HIS 0.002 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17992) covalent geometry : angle 0.51391 / 0.26 (24300) SS BOND : bond 0.00053 / 0.02 ( 4) SS BOND : angle 0.70770 / 0.39 ( 8) hydrogen bonds : bond 0.03684 / 2.37 ( 969) hydrogen bonds : angle 3.88936 / 2.70 ( 2811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4120 Ramachandran restraints generated. 2060 Oldfield, 0 Emsley, 2060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.539 Fit side-chains REVERT: A 270 TYR cc_start: 0.8055 (m-80) cc_final: 0.7738 (t80) REVERT: A 423 GLU cc_start: 0.8549 (tp30) cc_final: 0.8300 (tp30) REVERT: A 426 ASN cc_start: 0.8343 (m-40) cc_final: 0.7947 (m110) REVERT: A 436 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7634 (tp30) REVERT: A 478 GLU cc_start: 0.8142 (tp30) cc_final: 0.7734 (tp30) REVERT: A 481 MET cc_start: 0.8384 (mmt) cc_final: 0.8060 (mmm) REVERT: A 537 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7832 (ttm110) REVERT: A 586 ASP cc_start: 0.8682 (m-30) cc_final: 0.8279 (m-30) REVERT: B 262 TYR cc_start: 0.8695 (m-80) cc_final: 0.8408 (m-80) REVERT: B 270 TYR cc_start: 0.8044 (m-80) cc_final: 0.7746 (t80) REVERT: B 423 GLU cc_start: 0.8562 (tp30) cc_final: 0.8290 (tp30) REVERT: B 426 ASN cc_start: 0.8253 (m-40) cc_final: 0.7855 (m110) REVERT: B 436 GLU cc_start: 0.7985 (tp30) cc_final: 0.7711 (tp30) REVERT: B 438 ARG cc_start: 0.7672 (mpt180) cc_final: 0.7255 (mpt180) REVERT: B 478 GLU cc_start: 0.8146 (tp30) cc_final: 0.7786 (tp30) REVERT: B 535 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7990 (ttp80) REVERT: B 537 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7867 (ttm110) REVERT: C 262 TYR cc_start: 0.8688 (m-80) cc_final: 0.8401 (m-80) REVERT: C 423 GLU cc_start: 0.8575 (tp30) cc_final: 0.8301 (tp30) REVERT: C 426 ASN cc_start: 0.8261 (m-40) cc_final: 0.7875 (m110) REVERT: C 478 GLU cc_start: 0.8158 (tp30) cc_final: 0.7739 (tp30) REVERT: C 481 MET cc_start: 0.8412 (mmt) cc_final: 0.8084 (mmm) REVERT: C 537 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.7831 (ttm110) REVERT: C 586 ASP cc_start: 0.8643 (m-30) cc_final: 0.8214 (m-30) REVERT: D 270 TYR cc_start: 0.8031 (m-80) cc_final: 0.7766 (t80) REVERT: D 423 GLU cc_start: 0.8585 (tp30) cc_final: 0.8309 (tp30) REVERT: D 426 ASN cc_start: 0.8346 (m-40) cc_final: 0.7957 (m110) REVERT: D 478 GLU cc_start: 0.8183 (tp30) cc_final: 0.7790 (tp30) REVERT: D 481 MET cc_start: 0.8448 (mmt) cc_final: 0.8090 (mmm) REVERT: D 535 ARG cc_start: 0.8375 (ttp-110) cc_final: 0.7893 (ttp80) REVERT: D 537 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.7929 (ttm110) REVERT: D 586 ASP cc_start: 0.8789 (m-30) cc_final: 0.8503 (m-30) outliers start: 19 outliers final: 18 residues processed: 226 average time/residue: 0.1433 time to fit residues: 49.6155 Evaluate side-chains 224 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 557 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 129 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.175618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119389 restraints weight = 20723.676| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.99 r_work: 0.3183 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17996 Z= 0.112 Angle : 0.501 9.109 24308 Z= 0.254 Chirality : 0.040 0.169 2644 Planarity : 0.003 0.038 2960 Dihedral : 7.555 56.221 2620 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.18 % Allowed : 13.41 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 2060 helix: 1.42 (0.15), residues: 1212 sheet: 0.70 (0.46), residues: 120 loop : -0.16 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 580 TYR 0.010 0.001 TYR D 363 PHE 0.012 0.001 PHE C 328 TRP 0.011 0.001 TRP C 124 HIS 0.001 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (17992) covalent geometry : angle 0.50108 / 0.25 (24300) SS BOND : bond 0.00091 / 0.04 ( 4) SS BOND : angle 0.70097 / 0.38 ( 8) hydrogen bonds : bond 0.03498 / 2.25 ( 969) hydrogen bonds : angle 3.80865 / 2.64 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5023.09 seconds wall clock time: 86 minutes 48.24 seconds (5208.24 seconds total)