Starting phenix.real_space_refine on Tue Jul 29 19:13:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v6d_21071/07_2025/6v6d_21071.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v6d_21071/07_2025/6v6d_21071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v6d_21071/07_2025/6v6d_21071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v6d_21071/07_2025/6v6d_21071.map" model { file = "/net/cci-nas-00/data/ceres_data/6v6d_21071/07_2025/6v6d_21071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v6d_21071/07_2025/6v6d_21071.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7924 2.51 5 N 1778 2.21 5 O 1974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11739 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1677 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 10, 'TRANS': 198} Chain breaks: 3 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.06, per 1000 atoms: 0.35 Number of scatterers: 11739 At special positions: 0 Unit cell: (110, 110, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1974 8.00 N 1778 7.00 C 7924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 71.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.800A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 108 through 139 Proline residue: A 123 - end of helix removed outlier: 3.754A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.716A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.800A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 108 through 139 Proline residue: B 123 - end of helix removed outlier: 3.754A pdb=" N PHE B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Proline residue: B 133 - end of helix Processing helix chain 'B' and resid 208 through 237 removed outlier: 3.575A pdb=" N LEU B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 4.459A pdb=" N ASN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 3.716A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.799A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 86 Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 108 through 139 Proline residue: C 123 - end of helix removed outlier: 3.754A pdb=" N PHE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 130 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU C 237 " --> pdb=" O TYR C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.457A pdb=" N ASN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 removed outlier: 3.646A pdb=" N LEU C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Proline residue: C 289 - end of helix removed outlier: 3.716A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.800A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 108 through 139 Proline residue: D 123 - end of helix removed outlier: 3.754A pdb=" N PHE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 130 " --> pdb=" O PHE D 126 " (cutoff:3.500A) Proline residue: D 133 - end of helix Processing helix chain 'D' and resid 208 through 237 removed outlier: 3.575A pdb=" N LEU D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Proline residue: D 289 - end of helix removed outlier: 3.716A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.800A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 86 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 108 through 139 Proline residue: E 123 - end of helix removed outlier: 3.754A pdb=" N PHE E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 130 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Proline residue: E 133 - end of helix Processing helix chain 'E' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU E 237 " --> pdb=" O TYR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Proline residue: E 289 - end of helix removed outlier: 3.717A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.800A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 86 Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 108 through 139 Proline residue: F 123 - end of helix removed outlier: 3.754A pdb=" N PHE F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 130 " --> pdb=" O PHE F 126 " (cutoff:3.500A) Proline residue: F 133 - end of helix Processing helix chain 'F' and resid 208 through 237 removed outlier: 3.574A pdb=" N LEU F 237 " --> pdb=" O TYR F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 4.459A pdb=" N ASN F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Proline residue: F 289 - end of helix removed outlier: 3.716A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 336 removed outlier: 3.726A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.800A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 86 Processing helix chain 'G' and resid 103 through 108 Processing helix chain 'G' and resid 108 through 139 Proline residue: G 123 - end of helix removed outlier: 3.754A pdb=" N PHE G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 130 " --> pdb=" O PHE G 126 " (cutoff:3.500A) Proline residue: G 133 - end of helix Processing helix chain 'G' and resid 208 through 237 removed outlier: 3.575A pdb=" N LEU G 237 " --> pdb=" O TYR G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 4.458A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 removed outlier: 3.647A pdb=" N LEU G 286 " --> pdb=" O VAL G 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Proline residue: G 289 - end of helix removed outlier: 3.717A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 336 removed outlier: 3.725A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 728 hydrogen bonds defined for protein. 2121 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: 3.48 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3374 1.34 - 1.46: 2809 1.46 - 1.58: 5787 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 12040 Sorted by residual: bond pdb=" N ILE E 41 " pdb=" CA ILE E 41 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.11e+00 bond pdb=" N ILE B 41 " pdb=" CA ILE B 41 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.21e-02 6.83e+03 9.03e+00 bond pdb=" N ILE F 41 " pdb=" CA ILE F 41 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.21e-02 6.83e+03 9.03e+00 bond pdb=" N ILE D 41 " pdb=" CA ILE D 41 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.88e+00 bond pdb=" N ILE G 41 " pdb=" CA ILE G 41 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.85e+00 ... (remaining 12035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 15923 2.43 - 4.85: 391 4.85 - 7.28: 66 7.28 - 9.70: 35 9.70 - 12.13: 7 Bond angle restraints: 16422 Sorted by residual: angle pdb=" N GLY C 61 " pdb=" CA GLY C 61 " pdb=" C GLY C 61 " ideal model delta sigma weight residual 112.73 124.86 -12.13 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY G 61 " pdb=" CA GLY G 61 " pdb=" C GLY G 61 " ideal model delta sigma weight residual 112.73 124.86 -12.13 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY E 61 " pdb=" CA GLY E 61 " pdb=" C GLY E 61 " ideal model delta sigma weight residual 112.73 124.85 -12.12 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY F 61 " pdb=" CA GLY F 61 " pdb=" C GLY F 61 " ideal model delta sigma weight residual 112.73 124.83 -12.10 1.20e+00 6.94e-01 1.02e+02 angle pdb=" N GLY D 61 " pdb=" CA GLY D 61 " pdb=" C GLY D 61 " ideal model delta sigma weight residual 112.73 124.83 -12.10 1.20e+00 6.94e-01 1.02e+02 ... (remaining 16417 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 6405 17.09 - 34.18: 581 34.18 - 51.27: 77 51.27 - 68.36: 7 68.36 - 85.45: 7 Dihedral angle restraints: 7077 sinusoidal: 2709 harmonic: 4368 Sorted by residual: dihedral pdb=" C ASP B 35 " pdb=" N ASP B 35 " pdb=" CA ASP B 35 " pdb=" CB ASP B 35 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C ASP F 35 " pdb=" N ASP F 35 " pdb=" CA ASP F 35 " pdb=" CB ASP F 35 " ideal model delta harmonic sigma weight residual -122.60 -131.84 9.24 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C ASP A 35 " pdb=" N ASP A 35 " pdb=" CA ASP A 35 " pdb=" CB ASP A 35 " ideal model delta harmonic sigma weight residual -122.60 -131.82 9.22 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 7074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1559 0.057 - 0.114: 308 0.114 - 0.171: 107 0.171 - 0.229: 7 0.229 - 0.286: 14 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CA LEU D 32 " pdb=" N LEU D 32 " pdb=" C LEU D 32 " pdb=" CB LEU D 32 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA LEU C 32 " pdb=" N LEU C 32 " pdb=" C LEU C 32 " pdb=" CB LEU C 32 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA LEU B 32 " pdb=" N LEU B 32 " pdb=" C LEU B 32 " pdb=" CB LEU B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1992 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 132 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO E 133 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 133 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 133 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 132 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO G 133 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 133 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 133 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 132 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO F 133 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 133 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 133 " -0.035 5.00e-02 4.00e+02 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3326 2.80 - 3.33: 11144 3.33 - 3.85: 18671 3.85 - 4.38: 20454 4.38 - 4.90: 36759 Nonbonded interactions: 90354 Sorted by model distance: nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 52 " model vdw 2.307 3.040 nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.325 3.040 nonbonded pdb=" O SER D 241 " pdb=" OG SER D 241 " model vdw 2.350 3.040 ... (remaining 90349 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.130 Find NCS groups from input model: 0.270 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12054 Z= 0.307 Angle : 0.948 12.128 16450 Z= 0.571 Chirality : 0.058 0.286 1995 Planarity : 0.007 0.061 1953 Dihedral : 13.309 85.452 4179 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.20), residues: 1407 helix: -0.43 (0.15), residues: 1001 sheet: -2.75 (0.55), residues: 84 loop : -4.03 (0.18), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 74 HIS 0.001 0.000 HIS E 134 PHE 0.010 0.001 PHE G 129 TYR 0.009 0.001 TYR E 230 ARG 0.002 0.000 ARG C 254 Details of bonding type rmsd hydrogen bonds : bond 0.14117 ( 728) hydrogen bonds : angle 5.25097 ( 2121) SS BOND : bond 0.00104 ( 14) SS BOND : angle 1.11443 ( 28) covalent geometry : bond 0.00548 (12040) covalent geometry : angle 0.94751 (16422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8764 (tptt) cc_final: 0.8538 (tttt) REVERT: A 75 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8292 (mmt180) REVERT: A 212 LYS cc_start: 0.7283 (mttp) cc_final: 0.7010 (mttp) REVERT: A 326 ASN cc_start: 0.6408 (p0) cc_final: 0.5651 (p0) REVERT: B 36 LYS cc_start: 0.8908 (tptt) cc_final: 0.8494 (tttt) REVERT: B 293 TYR cc_start: 0.9148 (t80) cc_final: 0.8889 (t80) REVERT: B 326 ASN cc_start: 0.6800 (p0) cc_final: 0.5894 (p0) REVERT: B 333 LEU cc_start: 0.8827 (pp) cc_final: 0.8497 (pp) REVERT: C 36 LYS cc_start: 0.8986 (tptt) cc_final: 0.8585 (tttt) REVERT: C 126 PHE cc_start: 0.8798 (t80) cc_final: 0.8498 (t80) REVERT: C 275 LEU cc_start: 0.8998 (tt) cc_final: 0.8666 (tp) REVERT: C 326 ASN cc_start: 0.6433 (p0) cc_final: 0.5564 (p0) REVERT: C 327 ASP cc_start: 0.8749 (m-30) cc_final: 0.8495 (m-30) REVERT: C 333 LEU cc_start: 0.8664 (pp) cc_final: 0.8384 (pp) REVERT: D 36 LYS cc_start: 0.8900 (tptt) cc_final: 0.8631 (tttt) REVERT: D 75 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8270 (mmt180) REVERT: D 326 ASN cc_start: 0.6895 (p0) cc_final: 0.6028 (p0) REVERT: D 331 TYR cc_start: 0.8608 (m-80) cc_final: 0.8374 (m-80) REVERT: D 333 LEU cc_start: 0.8780 (pp) cc_final: 0.8361 (pp) REVERT: E 36 LYS cc_start: 0.8892 (tptt) cc_final: 0.8565 (tttt) REVERT: E 327 ASP cc_start: 0.8831 (m-30) cc_final: 0.8505 (m-30) REVERT: F 36 LYS cc_start: 0.9053 (tptt) cc_final: 0.8542 (tttt) REVERT: F 75 ARG cc_start: 0.8616 (mmm160) cc_final: 0.8296 (mmt180) REVERT: F 208 ASN cc_start: 0.8407 (p0) cc_final: 0.8171 (p0) REVERT: F 212 LYS cc_start: 0.7540 (mttp) cc_final: 0.7196 (mttt) REVERT: F 230 TYR cc_start: 0.9330 (t80) cc_final: 0.9076 (t80) REVERT: F 293 TYR cc_start: 0.9128 (t80) cc_final: 0.8675 (t80) REVERT: G 29 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7837 (mtm180) REVERT: G 36 LYS cc_start: 0.8877 (tptt) cc_final: 0.8609 (tttt) REVERT: G 212 LYS cc_start: 0.7452 (mttp) cc_final: 0.7081 (mttp) REVERT: G 326 ASN cc_start: 0.6795 (p0) cc_final: 0.5933 (p0) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2848 time to fit residues: 132.9727 Evaluate side-chains 251 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 332 ASN B 106 HIS B 332 ASN C 106 HIS D 106 HIS D 332 ASN E 106 HIS ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS G 106 HIS ** G 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.089490 restraints weight = 19808.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091898 restraints weight = 10630.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.093279 restraints weight = 7452.510| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12054 Z= 0.133 Angle : 0.643 8.071 16450 Z= 0.320 Chirality : 0.040 0.135 1995 Planarity : 0.005 0.049 1953 Dihedral : 4.159 15.824 1554 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.89 % Allowed : 15.19 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1407 helix: 0.99 (0.16), residues: 1001 sheet: -2.55 (0.51), residues: 84 loop : -3.18 (0.23), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 74 HIS 0.001 0.000 HIS C 106 PHE 0.018 0.001 PHE A 299 TYR 0.017 0.001 TYR E 213 ARG 0.003 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 728) hydrogen bonds : angle 3.90681 ( 2121) SS BOND : bond 0.00065 ( 14) SS BOND : angle 0.97994 ( 28) covalent geometry : bond 0.00297 (12040) covalent geometry : angle 0.64277 (16422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 320 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8994 (tptt) cc_final: 0.8575 (tttt) REVERT: A 75 ARG cc_start: 0.8541 (mmm160) cc_final: 0.8274 (mmt180) REVERT: A 76 GLN cc_start: 0.8279 (mt0) cc_final: 0.7909 (mt0) REVERT: A 326 ASN cc_start: 0.6271 (p0) cc_final: 0.5589 (p0) REVERT: B 29 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7702 (mtm180) REVERT: B 36 LYS cc_start: 0.9063 (tptt) cc_final: 0.8407 (tttt) REVERT: B 111 TYR cc_start: 0.8708 (m-10) cc_final: 0.7989 (m-10) REVERT: B 326 ASN cc_start: 0.6650 (p0) cc_final: 0.5894 (p0) REVERT: B 333 LEU cc_start: 0.8616 (pp) cc_final: 0.8409 (pp) REVERT: C 36 LYS cc_start: 0.9132 (tptt) cc_final: 0.8682 (tttt) REVERT: C 75 ARG cc_start: 0.8634 (mmm160) cc_final: 0.8262 (mmt180) REVERT: C 76 GLN cc_start: 0.8404 (mt0) cc_final: 0.8179 (mt0) REVERT: C 248 ILE cc_start: 0.9124 (pt) cc_final: 0.8914 (tp) REVERT: C 255 ASN cc_start: 0.8667 (p0) cc_final: 0.8446 (p0) REVERT: C 275 LEU cc_start: 0.8992 (tt) cc_final: 0.8615 (tp) REVERT: C 276 LEU cc_start: 0.9250 (mt) cc_final: 0.9049 (mt) REVERT: D 36 LYS cc_start: 0.9114 (tptt) cc_final: 0.8641 (tttt) REVERT: D 75 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8282 (mmt180) REVERT: D 83 TYR cc_start: 0.8630 (t80) cc_final: 0.8112 (t80) REVERT: D 212 LYS cc_start: 0.7758 (mttp) cc_final: 0.7417 (mttp) REVERT: D 326 ASN cc_start: 0.6784 (p0) cc_final: 0.6029 (p0) REVERT: D 333 LEU cc_start: 0.8553 (pp) cc_final: 0.8347 (pp) REVERT: E 36 LYS cc_start: 0.9122 (tptt) cc_final: 0.8598 (tttm) REVERT: E 37 MET cc_start: 0.7993 (tpt) cc_final: 0.7545 (tmm) REVERT: E 333 LEU cc_start: 0.8703 (pp) cc_final: 0.8361 (pp) REVERT: F 36 LYS cc_start: 0.9177 (tptt) cc_final: 0.8573 (tttt) REVERT: F 75 ARG cc_start: 0.8669 (mmm160) cc_final: 0.8311 (mmt180) REVERT: F 111 TYR cc_start: 0.8892 (m-10) cc_final: 0.7880 (m-10) REVERT: F 276 LEU cc_start: 0.9235 (mt) cc_final: 0.9016 (mt) REVERT: G 36 LYS cc_start: 0.9099 (tptt) cc_final: 0.8698 (tttt) REVERT: G 75 ARG cc_start: 0.8518 (mmm160) cc_final: 0.8179 (mmt180) REVERT: G 326 ASN cc_start: 0.6530 (p0) cc_final: 0.5821 (p0) REVERT: G 334 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7652 (t80) outliers start: 25 outliers final: 15 residues processed: 334 average time/residue: 0.2856 time to fit residues: 128.9622 Evaluate side-chains 290 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 274 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN G 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.115984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.090162 restraints weight = 19726.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.092667 restraints weight = 10440.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.094179 restraints weight = 7276.618| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12054 Z= 0.118 Angle : 0.612 6.507 16450 Z= 0.300 Chirality : 0.039 0.136 1995 Planarity : 0.005 0.040 1953 Dihedral : 3.822 13.311 1554 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.57 % Allowed : 17.31 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1407 helix: 1.54 (0.17), residues: 1001 sheet: -2.48 (0.50), residues: 84 loop : -2.99 (0.25), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 74 HIS 0.001 0.000 HIS E 106 PHE 0.014 0.001 PHE C 126 TYR 0.018 0.001 TYR E 230 ARG 0.005 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 728) hydrogen bonds : angle 3.74576 ( 2121) SS BOND : bond 0.00047 ( 14) SS BOND : angle 0.75119 ( 28) covalent geometry : bond 0.00264 (12040) covalent geometry : angle 0.61180 (16422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 321 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9036 (tptt) cc_final: 0.8601 (tttt) REVERT: A 75 ARG cc_start: 0.8563 (mmm160) cc_final: 0.8304 (mmt180) REVERT: A 76 GLN cc_start: 0.8248 (mt0) cc_final: 0.7906 (mt0) REVERT: A 111 TYR cc_start: 0.8605 (m-10) cc_final: 0.8303 (m-10) REVERT: A 326 ASN cc_start: 0.6286 (p0) cc_final: 0.5529 (p0) REVERT: B 29 ARG cc_start: 0.7944 (ttp-110) cc_final: 0.7614 (mtm180) REVERT: B 36 LYS cc_start: 0.9033 (tptt) cc_final: 0.8393 (tttt) REVERT: B 111 TYR cc_start: 0.8617 (m-10) cc_final: 0.7902 (m-10) REVERT: B 212 LYS cc_start: 0.7995 (mttp) cc_final: 0.7491 (mttp) REVERT: B 326 ASN cc_start: 0.6728 (p0) cc_final: 0.5937 (p0) REVERT: C 36 LYS cc_start: 0.9158 (tptt) cc_final: 0.8690 (tttt) REVERT: C 75 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8353 (mmt180) REVERT: C 76 GLN cc_start: 0.8411 (mt0) cc_final: 0.8124 (mt0) REVERT: C 111 TYR cc_start: 0.8615 (m-10) cc_final: 0.8055 (m-10) REVERT: C 255 ASN cc_start: 0.8689 (p0) cc_final: 0.8445 (p0) REVERT: C 275 LEU cc_start: 0.8959 (tt) cc_final: 0.8579 (tp) REVERT: C 326 ASN cc_start: 0.6450 (p0) cc_final: 0.5750 (p0) REVERT: D 36 LYS cc_start: 0.9094 (tptt) cc_final: 0.8631 (tttt) REVERT: D 75 ARG cc_start: 0.8705 (mmm160) cc_final: 0.8305 (mmt180) REVERT: D 83 TYR cc_start: 0.8616 (t80) cc_final: 0.8106 (t80) REVERT: D 111 TYR cc_start: 0.8620 (m-10) cc_final: 0.7927 (m-10) REVERT: D 212 LYS cc_start: 0.7862 (mttp) cc_final: 0.7431 (mttp) REVERT: D 276 LEU cc_start: 0.9214 (mt) cc_final: 0.8966 (mt) REVERT: D 326 ASN cc_start: 0.6827 (p0) cc_final: 0.6019 (p0) REVERT: E 36 LYS cc_start: 0.9152 (tptt) cc_final: 0.8611 (tttm) REVERT: E 111 TYR cc_start: 0.8786 (m-10) cc_final: 0.7915 (m-10) REVERT: F 36 LYS cc_start: 0.9172 (tptt) cc_final: 0.8551 (tttt) REVERT: F 75 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8308 (mmt180) REVERT: F 111 TYR cc_start: 0.8818 (m-10) cc_final: 0.7901 (m-10) REVERT: G 36 LYS cc_start: 0.9094 (tptt) cc_final: 0.8682 (tttt) REVERT: G 75 ARG cc_start: 0.8535 (mmm160) cc_final: 0.8193 (mmt180) REVERT: G 111 TYR cc_start: 0.8741 (m-10) cc_final: 0.7973 (m-10) REVERT: G 326 ASN cc_start: 0.6717 (p0) cc_final: 0.5957 (p0) REVERT: G 334 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7715 (t80) outliers start: 34 outliers final: 27 residues processed: 332 average time/residue: 0.2643 time to fit residues: 118.8989 Evaluate side-chains 327 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 132 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.085992 restraints weight = 19698.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.088264 restraints weight = 10749.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.089483 restraints weight = 7725.526| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12054 Z= 0.184 Angle : 0.658 8.629 16450 Z= 0.319 Chirality : 0.041 0.134 1995 Planarity : 0.005 0.036 1953 Dihedral : 3.888 13.679 1554 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.72 % Allowed : 20.63 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1407 helix: 1.59 (0.17), residues: 1008 sheet: -2.36 (0.50), residues: 84 loop : -2.86 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 74 HIS 0.002 0.001 HIS E 106 PHE 0.016 0.001 PHE A 299 TYR 0.025 0.001 TYR F 230 ARG 0.004 0.001 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 728) hydrogen bonds : angle 4.09936 ( 2121) SS BOND : bond 0.00171 ( 14) SS BOND : angle 0.78502 ( 28) covalent geometry : bond 0.00446 (12040) covalent geometry : angle 0.65818 (16422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9027 (tptt) cc_final: 0.8603 (tttt) REVERT: A 75 ARG cc_start: 0.8626 (mmm160) cc_final: 0.8393 (mmt180) REVERT: A 76 GLN cc_start: 0.8333 (mt0) cc_final: 0.7930 (mt0) REVERT: A 111 TYR cc_start: 0.8713 (m-10) cc_final: 0.7869 (m-10) REVERT: A 326 ASN cc_start: 0.6630 (p0) cc_final: 0.5790 (p0) REVERT: B 36 LYS cc_start: 0.9044 (tptt) cc_final: 0.8537 (tttt) REVERT: B 111 TYR cc_start: 0.8777 (m-10) cc_final: 0.8114 (m-10) REVERT: B 212 LYS cc_start: 0.8166 (mttp) cc_final: 0.7896 (mttp) REVERT: B 326 ASN cc_start: 0.6880 (p0) cc_final: 0.6077 (p0) REVERT: C 36 LYS cc_start: 0.9138 (tptt) cc_final: 0.8703 (tttt) REVERT: C 75 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8383 (mmt180) REVERT: C 111 TYR cc_start: 0.8834 (m-10) cc_final: 0.8259 (m-10) REVERT: C 243 GLU cc_start: 0.8447 (pt0) cc_final: 0.8177 (pt0) REVERT: C 255 ASN cc_start: 0.8631 (p0) cc_final: 0.8381 (p0) REVERT: C 275 LEU cc_start: 0.9091 (tt) cc_final: 0.8678 (tp) REVERT: D 36 LYS cc_start: 0.9134 (tptt) cc_final: 0.8657 (tttt) REVERT: D 75 ARG cc_start: 0.8652 (mmm160) cc_final: 0.8241 (mmt180) REVERT: D 111 TYR cc_start: 0.8791 (m-10) cc_final: 0.8088 (m-10) REVERT: D 212 LYS cc_start: 0.7950 (mttp) cc_final: 0.7413 (mttp) REVERT: D 326 ASN cc_start: 0.7106 (p0) cc_final: 0.6346 (p0) REVERT: E 36 LYS cc_start: 0.9098 (tptt) cc_final: 0.8635 (tttt) REVERT: E 111 TYR cc_start: 0.8888 (m-10) cc_final: 0.8102 (m-10) REVERT: E 276 LEU cc_start: 0.9240 (mt) cc_final: 0.9016 (mt) REVERT: E 326 ASN cc_start: 0.6715 (p0) cc_final: 0.6073 (p0) REVERT: F 36 LYS cc_start: 0.9158 (tptt) cc_final: 0.8579 (tttt) REVERT: F 75 ARG cc_start: 0.8690 (mmm160) cc_final: 0.8322 (mmt180) REVERT: F 111 TYR cc_start: 0.8841 (m-10) cc_final: 0.7921 (m-10) REVERT: F 230 TYR cc_start: 0.9316 (t80) cc_final: 0.9001 (t80) REVERT: G 36 LYS cc_start: 0.9101 (tptt) cc_final: 0.8685 (tttt) REVERT: G 75 ARG cc_start: 0.8604 (mmm160) cc_final: 0.8328 (mmt180) REVERT: G 111 TYR cc_start: 0.8774 (m-10) cc_final: 0.8024 (m-10) REVERT: G 212 LYS cc_start: 0.7875 (mttp) cc_final: 0.7626 (mttp) REVERT: G 326 ASN cc_start: 0.7036 (p0) cc_final: 0.6416 (p0) REVERT: G 334 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7968 (t80) outliers start: 36 outliers final: 28 residues processed: 299 average time/residue: 0.2723 time to fit residues: 110.1755 Evaluate side-chains 295 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.088504 restraints weight = 19528.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.090895 restraints weight = 10584.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.092323 restraints weight = 7491.484| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12054 Z= 0.118 Angle : 0.597 6.704 16450 Z= 0.289 Chirality : 0.039 0.129 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.672 12.278 1554 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.02 % Allowed : 21.92 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1407 helix: 1.80 (0.17), residues: 1008 sheet: -2.30 (0.49), residues: 84 loop : -2.70 (0.28), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.001 0.000 HIS E 106 PHE 0.017 0.001 PHE G 299 TYR 0.021 0.001 TYR B 293 ARG 0.007 0.001 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.02894 ( 728) hydrogen bonds : angle 3.81329 ( 2121) SS BOND : bond 0.00036 ( 14) SS BOND : angle 0.51797 ( 28) covalent geometry : bond 0.00270 (12040) covalent geometry : angle 0.59708 (16422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9090 (tptt) cc_final: 0.8655 (tttt) REVERT: A 75 ARG cc_start: 0.8643 (mmm160) cc_final: 0.8402 (mmt180) REVERT: A 76 GLN cc_start: 0.8227 (mt0) cc_final: 0.7937 (mt0) REVERT: A 111 TYR cc_start: 0.8615 (m-10) cc_final: 0.7880 (m-10) REVERT: A 326 ASN cc_start: 0.6636 (p0) cc_final: 0.5823 (p0) REVERT: B 36 LYS cc_start: 0.9031 (tptt) cc_final: 0.8524 (tttt) REVERT: B 63 GLN cc_start: 0.7904 (mt0) cc_final: 0.7639 (mp10) REVERT: B 75 ARG cc_start: 0.8663 (mmm160) cc_final: 0.8385 (mmt180) REVERT: B 111 TYR cc_start: 0.8725 (m-10) cc_final: 0.8017 (m-10) REVERT: B 212 LYS cc_start: 0.8177 (mttp) cc_final: 0.7848 (mtmm) REVERT: B 326 ASN cc_start: 0.6844 (p0) cc_final: 0.6106 (p0) REVERT: C 36 LYS cc_start: 0.9095 (tptt) cc_final: 0.8696 (tttt) REVERT: C 75 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8428 (mmt180) REVERT: C 111 TYR cc_start: 0.8696 (m-10) cc_final: 0.8164 (m-10) REVERT: C 243 GLU cc_start: 0.8463 (pt0) cc_final: 0.8221 (pt0) REVERT: C 255 ASN cc_start: 0.8624 (p0) cc_final: 0.8352 (p0) REVERT: C 275 LEU cc_start: 0.8967 (tt) cc_final: 0.8531 (tp) REVERT: C 326 ASN cc_start: 0.6571 (p0) cc_final: 0.5961 (p0) REVERT: D 36 LYS cc_start: 0.9161 (tptt) cc_final: 0.8719 (tttt) REVERT: D 75 ARG cc_start: 0.8699 (mmm160) cc_final: 0.8252 (mmt180) REVERT: D 111 TYR cc_start: 0.8680 (m-10) cc_final: 0.7997 (m-10) REVERT: D 326 ASN cc_start: 0.6937 (p0) cc_final: 0.6146 (p0) REVERT: E 36 LYS cc_start: 0.9086 (tptt) cc_final: 0.8611 (tttm) REVERT: E 111 TYR cc_start: 0.8815 (m-10) cc_final: 0.7952 (m-10) REVERT: E 276 LEU cc_start: 0.9156 (mt) cc_final: 0.8940 (mt) REVERT: E 326 ASN cc_start: 0.6644 (p0) cc_final: 0.6022 (p0) REVERT: F 36 LYS cc_start: 0.9172 (tptt) cc_final: 0.8615 (tttt) REVERT: F 75 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8300 (mmt180) REVERT: F 111 TYR cc_start: 0.8759 (m-10) cc_final: 0.7896 (m-10) REVERT: F 230 TYR cc_start: 0.9323 (t80) cc_final: 0.9015 (t80) REVERT: G 29 ARG cc_start: 0.7382 (mtm110) cc_final: 0.7074 (mtm180) REVERT: G 36 LYS cc_start: 0.9113 (tptt) cc_final: 0.8660 (tttt) REVERT: G 75 ARG cc_start: 0.8632 (mmm160) cc_final: 0.8358 (mmt180) REVERT: G 111 TYR cc_start: 0.8681 (m-10) cc_final: 0.7923 (m-10) REVERT: G 301 GLN cc_start: 0.7486 (pp30) cc_final: 0.7264 (pp30) REVERT: G 326 ASN cc_start: 0.7065 (p0) cc_final: 0.6862 (p0) REVERT: G 334 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7865 (t80) outliers start: 40 outliers final: 32 residues processed: 319 average time/residue: 0.2750 time to fit residues: 119.8094 Evaluate side-chains 313 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 280 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN G 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.088849 restraints weight = 19672.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.091258 restraints weight = 10207.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.092614 restraints weight = 7105.669| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12054 Z= 0.116 Angle : 0.594 6.737 16450 Z= 0.287 Chirality : 0.039 0.130 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.538 11.572 1554 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.10 % Allowed : 22.83 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1407 helix: 1.92 (0.17), residues: 1008 sheet: -2.25 (0.48), residues: 84 loop : -2.59 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 85 HIS 0.001 0.000 HIS E 106 PHE 0.017 0.001 PHE C 299 TYR 0.022 0.001 TYR B 293 ARG 0.003 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 728) hydrogen bonds : angle 3.70728 ( 2121) SS BOND : bond 0.00048 ( 14) SS BOND : angle 0.63724 ( 28) covalent geometry : bond 0.00266 (12040) covalent geometry : angle 0.59368 (16422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9093 (tptt) cc_final: 0.8669 (tttt) REVERT: A 75 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8414 (mmt180) REVERT: A 76 GLN cc_start: 0.8215 (mt0) cc_final: 0.7964 (mt0) REVERT: A 111 TYR cc_start: 0.8607 (m-10) cc_final: 0.7860 (m-10) REVERT: A 301 GLN cc_start: 0.7675 (pp30) cc_final: 0.7462 (tm-30) REVERT: A 326 ASN cc_start: 0.6638 (p0) cc_final: 0.5922 (p0) REVERT: B 36 LYS cc_start: 0.9031 (tptt) cc_final: 0.8528 (tttt) REVERT: B 75 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8404 (mmt180) REVERT: B 111 TYR cc_start: 0.8689 (m-10) cc_final: 0.7918 (m-10) REVERT: B 212 LYS cc_start: 0.8179 (mttp) cc_final: 0.7795 (mtmm) REVERT: B 326 ASN cc_start: 0.6763 (p0) cc_final: 0.6061 (p0) REVERT: C 29 ARG cc_start: 0.7339 (mtm110) cc_final: 0.6972 (mtm-85) REVERT: C 36 LYS cc_start: 0.9105 (tptt) cc_final: 0.8740 (tttt) REVERT: C 75 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8406 (mmt180) REVERT: C 111 TYR cc_start: 0.8632 (m-10) cc_final: 0.8091 (m-10) REVERT: C 126 PHE cc_start: 0.8823 (t80) cc_final: 0.8520 (t80) REVERT: C 213 TYR cc_start: 0.8905 (t80) cc_final: 0.8668 (t80) REVERT: C 243 GLU cc_start: 0.8482 (pt0) cc_final: 0.8208 (pt0) REVERT: C 268 ILE cc_start: 0.9117 (mm) cc_final: 0.8870 (mm) REVERT: C 275 LEU cc_start: 0.8885 (tt) cc_final: 0.8498 (tp) REVERT: C 326 ASN cc_start: 0.6722 (p0) cc_final: 0.6108 (p0) REVERT: D 36 LYS cc_start: 0.9138 (tptt) cc_final: 0.8709 (tttt) REVERT: D 75 ARG cc_start: 0.8675 (mmm160) cc_final: 0.8240 (mmt180) REVERT: D 111 TYR cc_start: 0.8668 (m-10) cc_final: 0.8006 (m-10) REVERT: D 212 LYS cc_start: 0.8006 (mttp) cc_final: 0.7482 (mttp) REVERT: D 276 LEU cc_start: 0.9180 (mt) cc_final: 0.8962 (mt) REVERT: D 301 GLN cc_start: 0.7626 (pp30) cc_final: 0.7411 (pp30) REVERT: D 326 ASN cc_start: 0.6747 (p0) cc_final: 0.5960 (p0) REVERT: E 36 LYS cc_start: 0.9068 (tptt) cc_final: 0.8615 (tttt) REVERT: E 111 TYR cc_start: 0.8779 (m-10) cc_final: 0.7959 (m-10) REVERT: E 276 LEU cc_start: 0.9173 (mt) cc_final: 0.8944 (mt) REVERT: E 326 ASN cc_start: 0.6674 (p0) cc_final: 0.6038 (p0) REVERT: F 36 LYS cc_start: 0.9165 (tptt) cc_final: 0.8579 (tttt) REVERT: F 75 ARG cc_start: 0.8666 (mmm160) cc_final: 0.8263 (mmt180) REVERT: F 111 TYR cc_start: 0.8743 (m-10) cc_final: 0.7939 (m-10) REVERT: F 248 ILE cc_start: 0.8975 (pt) cc_final: 0.8700 (tp) REVERT: G 29 ARG cc_start: 0.7518 (mtm110) cc_final: 0.7223 (mtm180) REVERT: G 36 LYS cc_start: 0.9098 (tptt) cc_final: 0.8670 (tttt) REVERT: G 75 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8341 (mmt180) REVERT: G 111 TYR cc_start: 0.8678 (m-10) cc_final: 0.8003 (m-10) REVERT: G 212 LYS cc_start: 0.7906 (mttp) cc_final: 0.7595 (mttp) REVERT: G 301 GLN cc_start: 0.7846 (pp30) cc_final: 0.7587 (pp30) REVERT: G 326 ASN cc_start: 0.7097 (p0) cc_final: 0.6619 (p0) REVERT: G 334 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7905 (t80) outliers start: 41 outliers final: 31 residues processed: 307 average time/residue: 0.2715 time to fit residues: 113.0511 Evaluate side-chains 314 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.088745 restraints weight = 19912.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.091121 restraints weight = 10543.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.092620 restraints weight = 7391.027| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12054 Z= 0.119 Angle : 0.596 7.112 16450 Z= 0.289 Chirality : 0.039 0.129 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.498 11.020 1554 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.02 % Allowed : 23.51 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1407 helix: 1.94 (0.17), residues: 1008 sheet: -2.06 (0.49), residues: 84 loop : -2.45 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 85 HIS 0.001 0.000 HIS E 106 PHE 0.030 0.001 PHE G 126 TYR 0.023 0.001 TYR B 293 ARG 0.007 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.02685 ( 728) hydrogen bonds : angle 3.68018 ( 2121) SS BOND : bond 0.00412 ( 14) SS BOND : angle 1.05103 ( 28) covalent geometry : bond 0.00278 (12040) covalent geometry : angle 0.59515 (16422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9121 (tptt) cc_final: 0.8724 (tttt) REVERT: A 75 ARG cc_start: 0.8642 (mmm160) cc_final: 0.8380 (mmt180) REVERT: A 76 GLN cc_start: 0.8228 (mt0) cc_final: 0.7988 (mt0) REVERT: A 111 TYR cc_start: 0.8597 (m-10) cc_final: 0.7935 (m-10) REVERT: A 301 GLN cc_start: 0.7680 (pp30) cc_final: 0.7425 (tm-30) REVERT: A 326 ASN cc_start: 0.6663 (p0) cc_final: 0.5928 (p0) REVERT: B 36 LYS cc_start: 0.9031 (tptt) cc_final: 0.8532 (tttt) REVERT: B 75 ARG cc_start: 0.8662 (mmm160) cc_final: 0.8385 (mmt180) REVERT: B 111 TYR cc_start: 0.8667 (m-10) cc_final: 0.7956 (m-10) REVERT: B 212 LYS cc_start: 0.8227 (mttp) cc_final: 0.7813 (mtmm) REVERT: B 326 ASN cc_start: 0.6787 (p0) cc_final: 0.6106 (p0) REVERT: C 36 LYS cc_start: 0.9093 (tptt) cc_final: 0.8742 (tttt) REVERT: C 75 ARG cc_start: 0.8712 (mmm160) cc_final: 0.8497 (mmt180) REVERT: C 111 TYR cc_start: 0.8705 (m-10) cc_final: 0.8180 (m-10) REVERT: C 126 PHE cc_start: 0.8821 (t80) cc_final: 0.8519 (t80) REVERT: C 213 TYR cc_start: 0.8890 (t80) cc_final: 0.8651 (t80) REVERT: C 243 GLU cc_start: 0.8477 (pt0) cc_final: 0.8212 (pt0) REVERT: C 248 ILE cc_start: 0.9039 (pt) cc_final: 0.8744 (tp) REVERT: C 268 ILE cc_start: 0.9112 (mm) cc_final: 0.8859 (mm) REVERT: C 326 ASN cc_start: 0.6626 (p0) cc_final: 0.6043 (p0) REVERT: D 36 LYS cc_start: 0.9118 (tptt) cc_final: 0.8715 (tttt) REVERT: D 75 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8264 (mmt180) REVERT: D 111 TYR cc_start: 0.8668 (m-10) cc_final: 0.8036 (m-10) REVERT: D 212 LYS cc_start: 0.8034 (mttp) cc_final: 0.7573 (mttp) REVERT: D 301 GLN cc_start: 0.7816 (pp30) cc_final: 0.7543 (pp30) REVERT: D 326 ASN cc_start: 0.6766 (p0) cc_final: 0.5985 (p0) REVERT: E 36 LYS cc_start: 0.9082 (tptt) cc_final: 0.8632 (tttt) REVERT: E 111 TYR cc_start: 0.8781 (m-10) cc_final: 0.7937 (m-10) REVERT: E 326 ASN cc_start: 0.6715 (p0) cc_final: 0.6093 (p0) REVERT: F 36 LYS cc_start: 0.9152 (tptt) cc_final: 0.8625 (tttt) REVERT: F 75 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8260 (mmt180) REVERT: F 111 TYR cc_start: 0.8680 (m-10) cc_final: 0.7924 (m-10) REVERT: F 248 ILE cc_start: 0.8956 (pt) cc_final: 0.8690 (tp) REVERT: F 326 ASN cc_start: 0.7013 (p0) cc_final: 0.6215 (p0) REVERT: G 36 LYS cc_start: 0.9107 (tptt) cc_final: 0.8667 (tttt) REVERT: G 75 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8359 (mmt180) REVERT: G 111 TYR cc_start: 0.8642 (m-10) cc_final: 0.8053 (m-10) REVERT: G 212 LYS cc_start: 0.7887 (mttp) cc_final: 0.7380 (mttp) REVERT: G 301 GLN cc_start: 0.7906 (pp30) cc_final: 0.7553 (pp30) REVERT: G 326 ASN cc_start: 0.7132 (p0) cc_final: 0.6661 (p0) REVERT: G 334 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7932 (t80) outliers start: 40 outliers final: 36 residues processed: 302 average time/residue: 0.2705 time to fit residues: 109.9019 Evaluate side-chains 317 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.085175 restraints weight = 19986.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.087374 restraints weight = 11117.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.088580 restraints weight = 8004.890| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12054 Z= 0.201 Angle : 0.666 8.162 16450 Z= 0.325 Chirality : 0.041 0.128 1995 Planarity : 0.004 0.035 1953 Dihedral : 3.802 12.472 1554 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.33 % Allowed : 24.04 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1407 helix: 1.74 (0.17), residues: 1008 sheet: -1.87 (0.52), residues: 84 loop : -2.33 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 85 HIS 0.002 0.000 HIS E 106 PHE 0.019 0.001 PHE G 299 TYR 0.025 0.001 TYR B 293 ARG 0.008 0.001 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 728) hydrogen bonds : angle 4.08095 ( 2121) SS BOND : bond 0.00397 ( 14) SS BOND : angle 1.61478 ( 28) covalent geometry : bond 0.00488 (12040) covalent geometry : angle 0.66308 (16422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9098 (tptt) cc_final: 0.8729 (tttt) REVERT: A 76 GLN cc_start: 0.8297 (mt0) cc_final: 0.7982 (mt0) REVERT: A 111 TYR cc_start: 0.8704 (m-10) cc_final: 0.7973 (m-10) REVERT: A 326 ASN cc_start: 0.6915 (p0) cc_final: 0.6144 (p0) REVERT: B 36 LYS cc_start: 0.9020 (tptt) cc_final: 0.8545 (tttt) REVERT: B 75 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8438 (mmt180) REVERT: B 111 TYR cc_start: 0.8834 (m-10) cc_final: 0.8146 (m-10) REVERT: B 212 LYS cc_start: 0.8249 (mttp) cc_final: 0.7636 (mttp) REVERT: B 326 ASN cc_start: 0.7038 (p0) cc_final: 0.6255 (p0) REVERT: C 29 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7424 (mtm-85) REVERT: C 36 LYS cc_start: 0.9082 (tptt) cc_final: 0.8765 (tttt) REVERT: C 75 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8393 (mmt180) REVERT: C 111 TYR cc_start: 0.8837 (m-10) cc_final: 0.8361 (m-10) REVERT: D 36 LYS cc_start: 0.9140 (tptt) cc_final: 0.8733 (tttt) REVERT: D 75 ARG cc_start: 0.8710 (mmm160) cc_final: 0.8301 (mmt180) REVERT: D 111 TYR cc_start: 0.8833 (m-10) cc_final: 0.8108 (m-10) REVERT: D 212 LYS cc_start: 0.8152 (mttp) cc_final: 0.7649 (mttp) REVERT: D 301 GLN cc_start: 0.7784 (pp30) cc_final: 0.7472 (pp30) REVERT: D 326 ASN cc_start: 0.7190 (p0) cc_final: 0.6394 (p0) REVERT: E 36 LYS cc_start: 0.9046 (tptt) cc_final: 0.8608 (tttt) REVERT: E 111 TYR cc_start: 0.8941 (m-10) cc_final: 0.8082 (m-10) REVERT: E 326 ASN cc_start: 0.6849 (p0) cc_final: 0.6174 (p0) REVERT: F 36 LYS cc_start: 0.9181 (tptt) cc_final: 0.8654 (tttt) REVERT: F 75 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8299 (mmt180) REVERT: F 111 TYR cc_start: 0.8841 (m-10) cc_final: 0.8017 (m-10) REVERT: F 248 ILE cc_start: 0.9003 (pt) cc_final: 0.8765 (tp) REVERT: F 326 ASN cc_start: 0.7108 (p0) cc_final: 0.6325 (p0) REVERT: G 36 LYS cc_start: 0.9092 (tptt) cc_final: 0.8693 (tttt) REVERT: G 75 ARG cc_start: 0.8663 (mmm160) cc_final: 0.8380 (mmt180) REVERT: G 111 TYR cc_start: 0.8736 (m-10) cc_final: 0.8029 (m-10) REVERT: G 212 LYS cc_start: 0.7914 (mttp) cc_final: 0.7400 (mttp) REVERT: G 301 GLN cc_start: 0.7917 (pp30) cc_final: 0.7602 (pp30) REVERT: G 326 ASN cc_start: 0.7336 (p0) cc_final: 0.6885 (p0) REVERT: G 334 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7993 (t80) outliers start: 44 outliers final: 32 residues processed: 298 average time/residue: 0.2842 time to fit residues: 114.4053 Evaluate side-chains 298 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 24 optimal weight: 0.0870 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.087968 restraints weight = 19699.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.090283 restraints weight = 10359.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.091656 restraints weight = 7272.597| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12054 Z= 0.121 Angle : 0.616 7.420 16450 Z= 0.300 Chirality : 0.039 0.126 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.573 11.645 1554 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.49 % Allowed : 25.55 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1407 helix: 1.90 (0.17), residues: 1008 sheet: -1.85 (0.52), residues: 84 loop : -2.25 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 85 HIS 0.001 0.000 HIS G 106 PHE 0.026 0.001 PHE G 126 TYR 0.025 0.001 TYR B 293 ARG 0.008 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.02707 ( 728) hydrogen bonds : angle 3.75538 ( 2121) SS BOND : bond 0.00154 ( 14) SS BOND : angle 1.18570 ( 28) covalent geometry : bond 0.00280 (12040) covalent geometry : angle 0.61472 (16422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9110 (tptt) cc_final: 0.8706 (tttt) REVERT: A 76 GLN cc_start: 0.8258 (mt0) cc_final: 0.7981 (mt0) REVERT: A 111 TYR cc_start: 0.8634 (m-10) cc_final: 0.7941 (m-10) REVERT: A 326 ASN cc_start: 0.6737 (p0) cc_final: 0.5993 (p0) REVERT: A 328 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8436 (tt) REVERT: B 36 LYS cc_start: 0.9059 (tptt) cc_final: 0.8568 (tttt) REVERT: B 75 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8406 (mmt180) REVERT: B 111 TYR cc_start: 0.8710 (m-10) cc_final: 0.7995 (m-10) REVERT: B 301 GLN cc_start: 0.7958 (pp30) cc_final: 0.7756 (pp30) REVERT: B 326 ASN cc_start: 0.6778 (p0) cc_final: 0.6086 (p0) REVERT: C 36 LYS cc_start: 0.9106 (tptt) cc_final: 0.8755 (tttt) REVERT: C 75 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8460 (mmt180) REVERT: C 111 TYR cc_start: 0.8686 (m-10) cc_final: 0.8197 (m-10) REVERT: C 126 PHE cc_start: 0.8897 (t80) cc_final: 0.8582 (t80) REVERT: C 326 ASN cc_start: 0.6681 (p0) cc_final: 0.6150 (p0) REVERT: D 36 LYS cc_start: 0.9150 (tptt) cc_final: 0.8712 (tttt) REVERT: D 75 ARG cc_start: 0.8743 (mmm160) cc_final: 0.8296 (mmt180) REVERT: D 111 TYR cc_start: 0.8719 (m-10) cc_final: 0.8079 (m-10) REVERT: D 208 ASN cc_start: 0.8248 (p0) cc_final: 0.7950 (p0) REVERT: D 212 LYS cc_start: 0.8121 (mttp) cc_final: 0.7534 (mttp) REVERT: D 301 GLN cc_start: 0.7943 (pp30) cc_final: 0.7625 (pp30) REVERT: D 326 ASN cc_start: 0.6730 (p0) cc_final: 0.6054 (p0) REVERT: E 36 LYS cc_start: 0.9057 (tptt) cc_final: 0.8604 (tttt) REVERT: E 111 TYR cc_start: 0.8785 (m-10) cc_final: 0.7931 (m-10) REVERT: E 326 ASN cc_start: 0.6673 (p0) cc_final: 0.6002 (p0) REVERT: F 36 LYS cc_start: 0.9146 (tptt) cc_final: 0.8596 (tttt) REVERT: F 75 ARG cc_start: 0.8685 (mmm160) cc_final: 0.8167 (mmt180) REVERT: F 111 TYR cc_start: 0.8696 (m-10) cc_final: 0.7952 (m-10) REVERT: F 248 ILE cc_start: 0.9010 (pt) cc_final: 0.8757 (tp) REVERT: F 326 ASN cc_start: 0.6966 (p0) cc_final: 0.6203 (p0) REVERT: G 36 LYS cc_start: 0.9124 (tptt) cc_final: 0.8672 (tttt) REVERT: G 75 ARG cc_start: 0.8703 (mmm160) cc_final: 0.8395 (mmt180) REVERT: G 81 ASP cc_start: 0.7667 (m-30) cc_final: 0.7017 (m-30) REVERT: G 111 TYR cc_start: 0.8610 (m-10) cc_final: 0.8009 (m-10) REVERT: G 212 LYS cc_start: 0.7913 (mttp) cc_final: 0.7384 (mttp) REVERT: G 301 GLN cc_start: 0.7831 (pp30) cc_final: 0.7415 (pp30) REVERT: G 326 ASN cc_start: 0.7221 (p0) cc_final: 0.6814 (p0) REVERT: G 334 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7928 (t80) outliers start: 33 outliers final: 31 residues processed: 305 average time/residue: 0.2846 time to fit residues: 117.1167 Evaluate side-chains 314 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 106 optimal weight: 0.0370 chunk 13 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.089446 restraints weight = 19510.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.091754 restraints weight = 10141.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.093213 restraints weight = 7037.575| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12054 Z= 0.115 Angle : 0.618 7.505 16450 Z= 0.300 Chirality : 0.039 0.134 1995 Planarity : 0.004 0.037 1953 Dihedral : 3.464 11.071 1554 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.72 % Allowed : 25.62 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.23), residues: 1407 helix: 2.04 (0.17), residues: 1001 sheet: -1.56 (0.52), residues: 84 loop : -2.35 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 74 HIS 0.000 0.000 HIS E 106 PHE 0.020 0.001 PHE D 299 TYR 0.027 0.001 TYR B 293 ARG 0.008 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.02501 ( 728) hydrogen bonds : angle 3.71334 ( 2121) SS BOND : bond 0.00139 ( 14) SS BOND : angle 1.25096 ( 28) covalent geometry : bond 0.00259 (12040) covalent geometry : angle 0.61594 (16422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9101 (tptt) cc_final: 0.8715 (tttt) REVERT: A 111 TYR cc_start: 0.8589 (m-10) cc_final: 0.7892 (m-10) REVERT: A 326 ASN cc_start: 0.6744 (p0) cc_final: 0.5995 (p0) REVERT: A 328 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8456 (tt) REVERT: B 36 LYS cc_start: 0.9034 (tptt) cc_final: 0.8563 (tttt) REVERT: B 75 ARG cc_start: 0.8697 (mmm160) cc_final: 0.8419 (mmt180) REVERT: B 81 ASP cc_start: 0.7544 (m-30) cc_final: 0.7079 (m-30) REVERT: B 111 TYR cc_start: 0.8644 (m-10) cc_final: 0.7943 (m-10) REVERT: B 326 ASN cc_start: 0.6747 (p0) cc_final: 0.6092 (p0) REVERT: C 36 LYS cc_start: 0.9062 (tptt) cc_final: 0.8738 (tttt) REVERT: C 75 ARG cc_start: 0.8694 (mmm160) cc_final: 0.8444 (mmt180) REVERT: C 111 TYR cc_start: 0.8651 (m-10) cc_final: 0.8101 (m-10) REVERT: C 126 PHE cc_start: 0.8819 (t80) cc_final: 0.8516 (t80) REVERT: C 213 TYR cc_start: 0.8847 (t80) cc_final: 0.8544 (t80) REVERT: C 268 ILE cc_start: 0.9048 (mm) cc_final: 0.8777 (mm) REVERT: C 326 ASN cc_start: 0.6613 (p0) cc_final: 0.6058 (p0) REVERT: D 36 LYS cc_start: 0.9112 (tptt) cc_final: 0.8700 (tttt) REVERT: D 75 ARG cc_start: 0.8781 (mmm160) cc_final: 0.8303 (mmt180) REVERT: D 111 TYR cc_start: 0.8626 (m-10) cc_final: 0.8091 (m-10) REVERT: D 208 ASN cc_start: 0.8241 (p0) cc_final: 0.8037 (p0) REVERT: D 212 LYS cc_start: 0.8116 (mttp) cc_final: 0.7543 (mtmm) REVERT: D 276 LEU cc_start: 0.9176 (mt) cc_final: 0.8948 (mt) REVERT: D 301 GLN cc_start: 0.7848 (pp30) cc_final: 0.7524 (pp30) REVERT: D 326 ASN cc_start: 0.6723 (p0) cc_final: 0.6056 (p0) REVERT: E 29 ARG cc_start: 0.6987 (mtm110) cc_final: 0.6661 (ptp90) REVERT: E 36 LYS cc_start: 0.9036 (tptt) cc_final: 0.8613 (tttt) REVERT: E 81 ASP cc_start: 0.7629 (m-30) cc_final: 0.7150 (m-30) REVERT: E 111 TYR cc_start: 0.8757 (m-10) cc_final: 0.7920 (m-10) REVERT: E 326 ASN cc_start: 0.6643 (p0) cc_final: 0.5999 (p0) REVERT: F 29 ARG cc_start: 0.7269 (mtm110) cc_final: 0.6993 (ptp90) REVERT: F 36 LYS cc_start: 0.9117 (tptt) cc_final: 0.8660 (tttt) REVERT: F 75 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8223 (mmt180) REVERT: F 111 TYR cc_start: 0.8691 (m-10) cc_final: 0.7984 (m-10) REVERT: F 248 ILE cc_start: 0.9036 (pt) cc_final: 0.8748 (tp) REVERT: F 326 ASN cc_start: 0.6898 (p0) cc_final: 0.6114 (p0) REVERT: G 36 LYS cc_start: 0.9104 (tptt) cc_final: 0.8679 (tttt) REVERT: G 75 ARG cc_start: 0.8714 (mmm160) cc_final: 0.8381 (mmt180) REVERT: G 81 ASP cc_start: 0.7570 (m-30) cc_final: 0.6934 (m-30) REVERT: G 111 TYR cc_start: 0.8550 (m-10) cc_final: 0.7982 (m-10) REVERT: G 212 LYS cc_start: 0.7888 (mttp) cc_final: 0.7365 (mttp) REVERT: G 301 GLN cc_start: 0.7715 (pp30) cc_final: 0.7244 (pp30) REVERT: G 326 ASN cc_start: 0.7113 (p0) cc_final: 0.6673 (p0) REVERT: G 334 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7963 (t80) outliers start: 36 outliers final: 33 residues processed: 308 average time/residue: 0.2748 time to fit residues: 114.3666 Evaluate side-chains 322 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 228 CYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 334 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 46 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.089629 restraints weight = 19466.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.091992 restraints weight = 10129.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.093320 restraints weight = 7034.424| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12054 Z= 0.117 Angle : 0.621 7.459 16450 Z= 0.301 Chirality : 0.039 0.133 1995 Planarity : 0.004 0.037 1953 Dihedral : 3.416 10.457 1554 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.95 % Allowed : 25.32 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1407 helix: 2.01 (0.17), residues: 994 sheet: -1.38 (0.52), residues: 84 loop : -2.15 (0.29), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 85 HIS 0.001 0.000 HIS E 106 PHE 0.029 0.001 PHE G 126 TYR 0.027 0.001 TYR B 293 ARG 0.005 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.02527 ( 728) hydrogen bonds : angle 3.69432 ( 2121) SS BOND : bond 0.00130 ( 14) SS BOND : angle 1.26958 ( 28) covalent geometry : bond 0.00270 (12040) covalent geometry : angle 0.61896 (16422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3657.86 seconds wall clock time: 64 minutes 7.09 seconds (3847.09 seconds total)