Starting phenix.real_space_refine on Thu Sep 26 00:11:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/09_2024/6v6d_21071.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/09_2024/6v6d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/09_2024/6v6d_21071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/09_2024/6v6d_21071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/09_2024/6v6d_21071.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v6d_21071/09_2024/6v6d_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.42, per 1000 atoms: 0.38 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=2, 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 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 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: 0.95 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: 2.95 Time building geometry restraints manager: 3.35 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: 6387 17.09 - 34.18: 563 34.18 - 51.27: 77 51.27 - 68.36: 7 68.36 - 85.45: 7 Dihedral angle restraints: 7041 sinusoidal: 2673 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 7038 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: 2.03 - 2.60: 103 2.60 - 3.18: 9900 3.18 - 3.75: 18145 3.75 - 4.33: 22875 4.33 - 4.90: 39367 Nonbonded interactions: 90390 Sorted by model distance: nonbonded pdb=" SG CYS B 66 " pdb=" SG CYS B 265 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 66 " pdb=" SG CYS C 265 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS F 66 " pdb=" SG CYS F 265 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS E 66 " pdb=" SG CYS E 265 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS G 66 " pdb=" SG CYS G 265 " model vdw 2.030 3.760 ... (remaining 90385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 24.440 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.530 ------------------------------------------------------------------------------- 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 12040 Z= 0.345 Angle : 0.948 12.128 16422 Z= 0.571 Chirality : 0.058 0.286 1995 Planarity : 0.007 0.061 1953 Dihedral : 13.309 85.452 4179 Min Nonbonded Distance : 2.030 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.293 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: 0.2890 time to fit residues: 134.3243 Evaluate side-chains 251 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12040 Z= 0.184 Angle : 0.636 8.159 16422 Z= 0.316 Chirality : 0.040 0.134 1995 Planarity : 0.005 0.049 1953 Dihedral : 4.098 15.417 1554 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.74 % Allowed : 15.72 % Favored : 82.54 % 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: -0.23 (0.22), residues: 1407 helix: 0.99 (0.17), residues: 1001 sheet: -2.20 (0.53), residues: 84 loop : -3.21 (0.23), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 74 HIS 0.001 0.000 HIS C 106 PHE 0.017 0.001 PHE A 299 TYR 0.017 0.001 TYR E 213 ARG 0.004 0.000 ARG B 29 *********************** 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 367 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 344 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9000 (tptt) cc_final: 0.8609 (tttt) REVERT: A 75 ARG cc_start: 0.8492 (mmm160) cc_final: 0.8272 (mmt180) REVERT: A 76 GLN cc_start: 0.8271 (mt0) cc_final: 0.7929 (mt0) REVERT: A 326 ASN cc_start: 0.6245 (p0) cc_final: 0.5567 (p0) REVERT: B 29 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7685 (mtm180) REVERT: B 36 LYS cc_start: 0.9062 (tptt) cc_final: 0.8435 (tttt) REVERT: B 111 TYR cc_start: 0.8677 (m-10) cc_final: 0.7959 (m-10) REVERT: B 265 CYS cc_start: 0.7749 (m) cc_final: 0.6953 (m) REVERT: B 326 ASN cc_start: 0.6629 (p0) cc_final: 0.5861 (p0) REVERT: B 333 LEU cc_start: 0.8609 (pp) cc_final: 0.8403 (pp) REVERT: C 36 LYS cc_start: 0.9134 (tptt) cc_final: 0.8707 (tttt) REVERT: C 66 CYS cc_start: 0.7476 (m) cc_final: 0.7206 (m) REVERT: C 75 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8291 (mmt180) REVERT: C 76 GLN cc_start: 0.8422 (mt0) cc_final: 0.8158 (mt0) REVERT: C 84 CYS cc_start: 0.8199 (m) cc_final: 0.7384 (m) REVERT: C 126 PHE cc_start: 0.8857 (t80) cc_final: 0.8534 (t80) REVERT: C 246 CYS cc_start: 0.8668 (t) cc_final: 0.8379 (p) REVERT: C 255 ASN cc_start: 0.8718 (p0) cc_final: 0.8494 (p0) REVERT: C 265 CYS cc_start: 0.7656 (m) cc_final: 0.7172 (m) REVERT: C 275 LEU cc_start: 0.8998 (tt) cc_final: 0.8611 (tp) REVERT: C 276 LEU cc_start: 0.9241 (mt) cc_final: 0.9038 (mt) REVERT: D 36 LYS cc_start: 0.9124 (tptt) cc_final: 0.8669 (tttt) REVERT: D 66 CYS cc_start: 0.7542 (m) cc_final: 0.7184 (m) REVERT: D 75 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8258 (mmt180) REVERT: D 83 TYR cc_start: 0.8773 (t80) cc_final: 0.8355 (t80) REVERT: D 212 LYS cc_start: 0.7771 (mttp) cc_final: 0.7406 (mttp) REVERT: D 265 CYS cc_start: 0.7704 (m) cc_final: 0.7204 (m) REVERT: D 326 ASN cc_start: 0.6738 (p0) cc_final: 0.5974 (p0) REVERT: E 36 LYS cc_start: 0.9132 (tptt) cc_final: 0.8641 (tttm) REVERT: E 37 MET cc_start: 0.8002 (tpt) cc_final: 0.7663 (tmm) REVERT: E 66 CYS cc_start: 0.7512 (m) cc_final: 0.7014 (m) REVERT: E 265 CYS cc_start: 0.7509 (m) cc_final: 0.7091 (m) REVERT: E 333 LEU cc_start: 0.8645 (pp) cc_final: 0.8331 (pp) REVERT: F 36 LYS cc_start: 0.9159 (tptt) cc_final: 0.8593 (tttt) REVERT: F 75 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8298 (mmt180) REVERT: F 84 CYS cc_start: 0.8055 (m) cc_final: 0.7110 (m) REVERT: F 111 TYR cc_start: 0.8879 (m-10) cc_final: 0.7848 (m-10) REVERT: F 265 CYS cc_start: 0.7836 (m) cc_final: 0.7245 (m) REVERT: F 276 LEU cc_start: 0.9261 (mt) cc_final: 0.9035 (mt) REVERT: G 36 LYS cc_start: 0.9093 (tptt) cc_final: 0.8704 (tttt) REVERT: G 75 ARG cc_start: 0.8496 (mmm160) cc_final: 0.8220 (mmt180) REVERT: G 265 CYS cc_start: 0.7909 (m) cc_final: 0.7653 (m) REVERT: G 326 ASN cc_start: 0.6485 (p0) cc_final: 0.5772 (p0) REVERT: G 334 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7680 (t80) outliers start: 23 outliers final: 13 residues processed: 356 average time/residue: 0.2684 time to fit residues: 129.5355 Evaluate side-chains 305 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 291 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 70 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12040 Z= 0.170 Angle : 0.610 6.482 16422 Z= 0.299 Chirality : 0.039 0.135 1995 Planarity : 0.005 0.040 1953 Dihedral : 3.803 13.024 1554 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.57 % Allowed : 18.97 % Favored : 78.46 % 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: 0.53 (0.23), residues: 1407 helix: 1.54 (0.17), residues: 1001 sheet: -1.85 (0.53), residues: 84 loop : -2.94 (0.25), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 74 HIS 0.001 0.000 HIS E 106 PHE 0.014 0.001 PHE G 126 TYR 0.018 0.001 TYR B 293 ARG 0.004 0.000 ARG C 29 *********************** 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 371 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 337 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9034 (tptt) cc_final: 0.8617 (tttt) REVERT: A 75 ARG cc_start: 0.8493 (mmm160) cc_final: 0.8286 (mmt180) REVERT: A 76 GLN cc_start: 0.8284 (mt0) cc_final: 0.7930 (mt0) REVERT: A 111 TYR cc_start: 0.8595 (m-10) cc_final: 0.7838 (m-10) REVERT: A 326 ASN cc_start: 0.6268 (p0) cc_final: 0.5521 (p0) REVERT: B 36 LYS cc_start: 0.9013 (tptt) cc_final: 0.8502 (tttt) REVERT: B 111 TYR cc_start: 0.8593 (m-10) cc_final: 0.7893 (m-10) REVERT: B 212 LYS cc_start: 0.7949 (mttp) cc_final: 0.7455 (mttp) REVERT: B 326 ASN cc_start: 0.6697 (p0) cc_final: 0.5905 (p0) REVERT: C 36 LYS cc_start: 0.9157 (tptt) cc_final: 0.8717 (tttt) REVERT: C 66 CYS cc_start: 0.7511 (m) cc_final: 0.7137 (m) REVERT: C 75 ARG cc_start: 0.8607 (mmm160) cc_final: 0.8297 (mmt180) REVERT: C 76 GLN cc_start: 0.8445 (mt0) cc_final: 0.8142 (mt0) REVERT: C 111 TYR cc_start: 0.8602 (m-10) cc_final: 0.8035 (m-10) REVERT: C 255 ASN cc_start: 0.8706 (p0) cc_final: 0.8474 (p0) REVERT: C 265 CYS cc_start: 0.7605 (m) cc_final: 0.6976 (m) REVERT: C 275 LEU cc_start: 0.8971 (tt) cc_final: 0.8589 (tp) REVERT: C 326 ASN cc_start: 0.6453 (p0) cc_final: 0.5728 (p0) REVERT: D 36 LYS cc_start: 0.9105 (tptt) cc_final: 0.8645 (tttt) REVERT: D 66 CYS cc_start: 0.7439 (m) cc_final: 0.6636 (m) REVERT: D 75 ARG cc_start: 0.8654 (mmm160) cc_final: 0.8251 (mmt180) REVERT: D 111 TYR cc_start: 0.8609 (m-10) cc_final: 0.7911 (m-10) REVERT: D 212 LYS cc_start: 0.7864 (mttp) cc_final: 0.7417 (mttp) REVERT: D 265 CYS cc_start: 0.7780 (m) cc_final: 0.7174 (m) REVERT: D 276 LEU cc_start: 0.9213 (mt) cc_final: 0.8959 (mt) REVERT: D 326 ASN cc_start: 0.6775 (p0) cc_final: 0.5985 (p0) REVERT: E 36 LYS cc_start: 0.9149 (tptt) cc_final: 0.8642 (tttm) REVERT: E 66 CYS cc_start: 0.7559 (m) cc_final: 0.6800 (m) REVERT: E 111 TYR cc_start: 0.8768 (m-10) cc_final: 0.7909 (m-10) REVERT: E 265 CYS cc_start: 0.7548 (m) cc_final: 0.7323 (m) REVERT: E 276 LEU cc_start: 0.9262 (mt) cc_final: 0.9054 (mt) REVERT: F 36 LYS cc_start: 0.9170 (tptt) cc_final: 0.8580 (tttt) REVERT: F 75 ARG cc_start: 0.8690 (mmm160) cc_final: 0.8329 (mmt180) REVERT: F 84 CYS cc_start: 0.7363 (m) cc_final: 0.7086 (m) REVERT: F 111 TYR cc_start: 0.8782 (m-10) cc_final: 0.7888 (m-10) REVERT: G 36 LYS cc_start: 0.9098 (tptt) cc_final: 0.8721 (tttt) REVERT: G 75 ARG cc_start: 0.8485 (mmm160) cc_final: 0.8229 (mmt180) REVERT: G 111 TYR cc_start: 0.8724 (m-10) cc_final: 0.7948 (m-10) REVERT: G 326 ASN cc_start: 0.6691 (p0) cc_final: 0.5919 (p0) REVERT: G 334 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7729 (t80) outliers start: 34 outliers final: 27 residues processed: 350 average time/residue: 0.2671 time to fit residues: 128.3342 Evaluate side-chains 335 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 307 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE 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 297 VAL Chi-restraints excluded: chain A residue 335 LEU 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 105 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 43 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 125 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.0370 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12040 Z= 0.190 Angle : 0.614 8.645 16422 Z= 0.296 Chirality : 0.039 0.133 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.688 12.320 1554 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.95 % Allowed : 20.63 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1407 helix: 1.76 (0.17), residues: 994 sheet: -1.87 (0.50), residues: 84 loop : -2.71 (0.26), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 85 HIS 0.001 0.000 HIS E 106 PHE 0.014 0.001 PHE G 126 TYR 0.020 0.001 TYR B 293 ARG 0.005 0.000 ARG B 300 *********************** 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 373 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 334 time to evaluate : 1.334 Fit side-chains 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: 0.8608 (tttt) REVERT: A 75 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8286 (mmt180) REVERT: A 76 GLN cc_start: 0.8281 (mt0) cc_final: 0.7932 (mt0) REVERT: A 111 TYR cc_start: 0.8608 (m-10) cc_final: 0.7825 (m-10) REVERT: A 326 ASN cc_start: 0.6570 (p0) cc_final: 0.5756 (p0) REVERT: B 36 LYS cc_start: 0.9017 (tptt) cc_final: 0.8456 (tttt) REVERT: B 75 ARG cc_start: 0.8707 (mmm160) cc_final: 0.8442 (mmt180) REVERT: B 111 TYR cc_start: 0.8664 (m-10) cc_final: 0.7918 (m-10) REVERT: B 326 ASN cc_start: 0.6765 (p0) cc_final: 0.5994 (p0) REVERT: C 36 LYS cc_start: 0.9138 (tptt) cc_final: 0.8730 (tttt) REVERT: C 66 CYS cc_start: 0.7691 (m) cc_final: 0.7080 (m) REVERT: C 75 ARG cc_start: 0.8694 (mmm160) cc_final: 0.8388 (mmt180) REVERT: C 111 TYR cc_start: 0.8636 (m-10) cc_final: 0.8066 (m-10) REVERT: C 213 TYR cc_start: 0.8865 (t80) cc_final: 0.8637 (t80) REVERT: C 255 ASN cc_start: 0.8695 (p0) cc_final: 0.8427 (p0) REVERT: C 265 CYS cc_start: 0.7522 (m) cc_final: 0.7301 (m) REVERT: C 275 LEU cc_start: 0.8982 (tt) cc_final: 0.8573 (tp) REVERT: C 326 ASN cc_start: 0.6513 (p0) cc_final: 0.5823 (p0) REVERT: D 36 LYS cc_start: 0.9126 (tptt) cc_final: 0.8675 (tttt) REVERT: D 75 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8297 (mmt180) REVERT: D 111 TYR cc_start: 0.8647 (m-10) cc_final: 0.7980 (m-10) REVERT: D 212 LYS cc_start: 0.7912 (mttp) cc_final: 0.7421 (mttp) REVERT: D 276 LEU cc_start: 0.9203 (mt) cc_final: 0.8972 (mt) REVERT: D 326 ASN cc_start: 0.6750 (p0) cc_final: 0.5939 (p0) REVERT: E 36 LYS cc_start: 0.9104 (tptt) cc_final: 0.8649 (tttt) REVERT: E 111 TYR cc_start: 0.8775 (m-10) cc_final: 0.7927 (m-10) REVERT: E 326 ASN cc_start: 0.6621 (p0) cc_final: 0.5996 (p0) REVERT: F 36 LYS cc_start: 0.9151 (tptt) cc_final: 0.8581 (tttt) REVERT: F 75 ARG cc_start: 0.8655 (mmm160) cc_final: 0.8328 (mmt180) REVERT: F 111 TYR cc_start: 0.8737 (m-10) cc_final: 0.7868 (m-10) REVERT: G 36 LYS cc_start: 0.9119 (tptt) cc_final: 0.8708 (tttt) REVERT: G 75 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8398 (mmt180) REVERT: G 111 TYR cc_start: 0.8681 (m-10) cc_final: 0.7910 (m-10) REVERT: G 326 ASN cc_start: 0.6886 (p0) cc_final: 0.6123 (p0) REVERT: G 334 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7941 (t80) outliers start: 39 outliers final: 31 residues processed: 349 average time/residue: 0.2640 time to fit residues: 125.2046 Evaluate side-chains 336 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 304 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain A residue 335 LEU 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 265 CYS Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 105 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 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 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 105 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 301 GLN G 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12040 Z= 0.254 Angle : 0.642 8.119 16422 Z= 0.311 Chirality : 0.040 0.132 1995 Planarity : 0.004 0.035 1953 Dihedral : 3.764 12.975 1554 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.55 % Allowed : 21.92 % Favored : 74.53 % 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: 1.83 (0.17), residues: 1001 sheet: -1.70 (0.51), residues: 84 loop : -2.61 (0.28), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 85 HIS 0.002 0.000 HIS E 106 PHE 0.018 0.001 PHE A 299 TYR 0.022 0.001 TYR B 293 ARG 0.007 0.001 ARG C 29 *********************** 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 340 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 293 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9023 (tptt) cc_final: 0.8604 (tttt) REVERT: A 75 ARG cc_start: 0.8632 (mmm160) cc_final: 0.8394 (mmt180) REVERT: A 76 GLN cc_start: 0.8340 (mt0) cc_final: 0.7961 (mt0) REVERT: A 111 TYR cc_start: 0.8694 (m-10) cc_final: 0.7910 (m-10) REVERT: A 326 ASN cc_start: 0.6623 (p0) cc_final: 0.5766 (p0) REVERT: B 36 LYS cc_start: 0.9018 (tptt) cc_final: 0.8541 (tttt) REVERT: B 75 ARG cc_start: 0.8712 (mmm160) cc_final: 0.8458 (mmt180) REVERT: B 111 TYR cc_start: 0.8756 (m-10) cc_final: 0.8014 (m-10) REVERT: B 212 LYS cc_start: 0.7939 (mttp) cc_final: 0.7422 (mttp) REVERT: B 326 ASN cc_start: 0.6851 (p0) cc_final: 0.6006 (p0) REVERT: C 36 LYS cc_start: 0.9143 (tptt) cc_final: 0.8749 (tttt) REVERT: C 75 ARG cc_start: 0.8697 (mmm160) cc_final: 0.8444 (mmt180) REVERT: C 111 TYR cc_start: 0.8794 (m-10) cc_final: 0.8272 (m-10) REVERT: C 255 ASN cc_start: 0.8679 (p0) cc_final: 0.8428 (p0) REVERT: D 36 LYS cc_start: 0.9169 (tptt) cc_final: 0.8703 (tttt) REVERT: D 75 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8285 (mmt180) REVERT: D 111 TYR cc_start: 0.8741 (m-10) cc_final: 0.8051 (m-10) REVERT: D 212 LYS cc_start: 0.7990 (mttp) cc_final: 0.7402 (mttp) REVERT: D 326 ASN cc_start: 0.6937 (p0) cc_final: 0.6091 (p0) REVERT: E 36 LYS cc_start: 0.9078 (tptt) cc_final: 0.8642 (tttt) REVERT: E 111 TYR cc_start: 0.8866 (m-10) cc_final: 0.8019 (m-10) REVERT: E 276 LEU cc_start: 0.9207 (mt) cc_final: 0.8984 (mt) REVERT: E 326 ASN cc_start: 0.6733 (p0) cc_final: 0.6067 (p0) REVERT: F 36 LYS cc_start: 0.9165 (tptt) cc_final: 0.8592 (tttt) REVERT: F 75 ARG cc_start: 0.8686 (mmm160) cc_final: 0.8354 (mmt180) REVERT: F 111 TYR cc_start: 0.8758 (m-10) cc_final: 0.7795 (m-10) REVERT: G 36 LYS cc_start: 0.9091 (tptt) cc_final: 0.8672 (tttt) REVERT: G 75 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8268 (mmt180) REVERT: G 111 TYR cc_start: 0.8703 (m-10) cc_final: 0.7949 (m-10) REVERT: G 212 LYS cc_start: 0.7885 (mttp) cc_final: 0.7596 (mttp) REVERT: G 301 GLN cc_start: 0.7540 (pp30) cc_final: 0.7315 (pp30) REVERT: G 326 ASN cc_start: 0.7046 (p0) cc_final: 0.6350 (p0) REVERT: G 334 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7888 (t80) outliers start: 47 outliers final: 35 residues processed: 317 average time/residue: 0.2938 time to fit residues: 127.0719 Evaluate side-chains 320 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 284 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 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 248 ILE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 105 LEU 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 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 297 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 105 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12040 Z= 0.201 Angle : 0.612 7.021 16422 Z= 0.297 Chirality : 0.039 0.127 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.670 15.529 1554 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.55 % Allowed : 23.36 % Favored : 73.09 % 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: 1.12 (0.23), residues: 1407 helix: 1.86 (0.17), residues: 1008 sheet: -1.67 (0.51), residues: 84 loop : -2.32 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 85 HIS 0.001 0.000 HIS E 106 PHE 0.019 0.001 PHE D 299 TYR 0.022 0.001 TYR B 293 ARG 0.003 0.000 ARG D 128 *********************** 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 351 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 304 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9092 (tptt) cc_final: 0.8687 (tttt) REVERT: A 75 ARG cc_start: 0.8526 (mmm160) cc_final: 0.8311 (mmt180) REVERT: A 76 GLN cc_start: 0.8275 (mt0) cc_final: 0.7980 (mt0) REVERT: A 111 TYR cc_start: 0.8599 (m-10) cc_final: 0.7915 (m-10) REVERT: A 326 ASN cc_start: 0.6675 (p0) cc_final: 0.5839 (p0) REVERT: B 36 LYS cc_start: 0.9010 (tptt) cc_final: 0.8549 (tttt) REVERT: B 75 ARG cc_start: 0.8655 (mmm160) cc_final: 0.8437 (mmt180) REVERT: B 212 LYS cc_start: 0.7989 (mttp) cc_final: 0.7436 (mttp) REVERT: B 247 SER cc_start: 0.8626 (t) cc_final: 0.8377 (m) REVERT: B 265 CYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8190 (m) REVERT: B 301 GLN cc_start: 0.7978 (pp30) cc_final: 0.7752 (pp30) REVERT: B 326 ASN cc_start: 0.6818 (p0) cc_final: 0.6080 (p0) REVERT: C 36 LYS cc_start: 0.9135 (tptt) cc_final: 0.8763 (tttt) REVERT: C 75 ARG cc_start: 0.8646 (mmm160) cc_final: 0.8439 (mmt180) REVERT: C 111 TYR cc_start: 0.8663 (m-10) cc_final: 0.8135 (m-10) REVERT: C 255 ASN cc_start: 0.8719 (p0) cc_final: 0.8419 (p0) REVERT: C 326 ASN cc_start: 0.6637 (p0) cc_final: 0.6016 (p0) REVERT: D 36 LYS cc_start: 0.9163 (tptt) cc_final: 0.8731 (tttt) REVERT: D 75 ARG cc_start: 0.8659 (mmm160) cc_final: 0.8266 (mmt180) REVERT: D 111 TYR cc_start: 0.8689 (m-10) cc_final: 0.7998 (m-10) REVERT: D 212 LYS cc_start: 0.8006 (mttp) cc_final: 0.7454 (mttp) REVERT: D 301 GLN cc_start: 0.7816 (pp30) cc_final: 0.7532 (pp30) REVERT: D 326 ASN cc_start: 0.6833 (p0) cc_final: 0.6006 (p0) REVERT: E 36 LYS cc_start: 0.9080 (tptt) cc_final: 0.8628 (tttm) REVERT: E 111 TYR cc_start: 0.8810 (m-10) cc_final: 0.7935 (m-10) REVERT: E 276 LEU cc_start: 0.9145 (mt) cc_final: 0.8914 (mt) REVERT: E 326 ASN cc_start: 0.6660 (p0) cc_final: 0.5997 (p0) REVERT: F 36 LYS cc_start: 0.9151 (tptt) cc_final: 0.8610 (tttt) REVERT: F 75 ARG cc_start: 0.8673 (mmm160) cc_final: 0.8338 (mmt180) REVERT: F 111 TYR cc_start: 0.8741 (m-10) cc_final: 0.7841 (m-10) REVERT: G 36 LYS cc_start: 0.9104 (tptt) cc_final: 0.8673 (tttt) REVERT: G 75 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8223 (mmt180) REVERT: G 111 TYR cc_start: 0.8713 (m-10) cc_final: 0.8049 (m-10) REVERT: G 212 LYS cc_start: 0.7967 (mttp) cc_final: 0.7692 (mttp) REVERT: G 301 GLN cc_start: 0.7859 (pp30) cc_final: 0.7585 (pp30) REVERT: G 326 ASN cc_start: 0.7104 (p0) cc_final: 0.6608 (p0) REVERT: G 334 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7935 (t80) outliers start: 47 outliers final: 39 residues processed: 323 average time/residue: 0.2676 time to fit residues: 117.6364 Evaluate side-chains 330 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 289 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 335 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 CYS 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 265 CYS Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 105 LEU 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 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 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 105 LEU Chi-restraints excluded: chain G residue 265 CYS 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 15 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12040 Z= 0.222 Angle : 0.623 7.161 16422 Z= 0.303 Chirality : 0.040 0.129 1995 Planarity : 0.004 0.036 1953 Dihedral : 3.655 16.588 1554 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.78 % Allowed : 23.05 % Favored : 73.17 % 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: 1.22 (0.23), residues: 1407 helix: 1.93 (0.17), residues: 1001 sheet: -1.51 (0.53), residues: 84 loop : -2.25 (0.30), residues: 322 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 0.034 0.001 PHE G 126 TYR 0.024 0.001 TYR B 293 ARG 0.003 0.000 ARG G 128 *********************** 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 352 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 302 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9122 (tptt) cc_final: 0.8726 (tttt) REVERT: A 75 ARG cc_start: 0.8532 (mmm160) cc_final: 0.8329 (mmt180) REVERT: A 76 GLN cc_start: 0.8316 (mt0) cc_final: 0.7989 (mt0) REVERT: A 111 TYR cc_start: 0.8582 (m-10) cc_final: 0.7903 (m-10) REVERT: A 301 GLN cc_start: 0.7650 (pp30) cc_final: 0.7421 (pp30) REVERT: A 326 ASN cc_start: 0.6708 (p0) cc_final: 0.5956 (p0) REVERT: B 36 LYS cc_start: 0.9038 (tptt) cc_final: 0.8545 (tttt) REVERT: B 75 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8433 (mmt180) REVERT: B 212 LYS cc_start: 0.7950 (mttp) cc_final: 0.7392 (mttp) REVERT: B 247 SER cc_start: 0.8655 (t) cc_final: 0.8416 (m) REVERT: B 265 CYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8244 (m) REVERT: B 301 GLN cc_start: 0.7982 (pp30) cc_final: 0.7734 (pp30) REVERT: B 326 ASN cc_start: 0.6836 (p0) cc_final: 0.6090 (p0) REVERT: C 36 LYS cc_start: 0.9120 (tptt) cc_final: 0.8779 (tttt) REVERT: C 75 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8450 (mmt180) REVERT: C 111 TYR cc_start: 0.8707 (m-10) cc_final: 0.8211 (m-10) REVERT: C 255 ASN cc_start: 0.8758 (p0) cc_final: 0.8494 (p0) REVERT: D 36 LYS cc_start: 0.9159 (tptt) cc_final: 0.8740 (tttt) REVERT: D 75 ARG cc_start: 0.8675 (mmm160) cc_final: 0.8316 (mmt180) REVERT: D 111 TYR cc_start: 0.8689 (m-10) cc_final: 0.8037 (m-10) REVERT: D 212 LYS cc_start: 0.8035 (mttp) cc_final: 0.7524 (mttp) REVERT: D 326 ASN cc_start: 0.6952 (p0) cc_final: 0.6109 (p0) REVERT: E 36 LYS cc_start: 0.9079 (tptt) cc_final: 0.8644 (tttt) REVERT: E 111 TYR cc_start: 0.8840 (m-10) cc_final: 0.7894 (m-10) REVERT: E 276 LEU cc_start: 0.9207 (mt) cc_final: 0.8985 (mt) REVERT: E 326 ASN cc_start: 0.6746 (p0) cc_final: 0.6079 (p0) REVERT: F 36 LYS cc_start: 0.9160 (tptt) cc_final: 0.8632 (tttt) REVERT: F 75 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8337 (mmt180) REVERT: F 111 TYR cc_start: 0.8767 (m-10) cc_final: 0.7916 (m-10) REVERT: F 326 ASN cc_start: 0.6934 (p0) cc_final: 0.6159 (p0) REVERT: G 36 LYS cc_start: 0.9098 (tptt) cc_final: 0.8694 (tttt) REVERT: G 75 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8200 (mmt180) REVERT: G 111 TYR cc_start: 0.8704 (m-10) cc_final: 0.8008 (m-10) REVERT: G 212 LYS cc_start: 0.7978 (mttp) cc_final: 0.7479 (mttp) REVERT: G 301 GLN cc_start: 0.7953 (pp30) cc_final: 0.7629 (pp30) REVERT: G 326 ASN cc_start: 0.7133 (p0) cc_final: 0.6642 (p0) REVERT: G 334 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.7989 (t80) outliers start: 50 outliers final: 41 residues processed: 321 average time/residue: 0.2688 time to fit residues: 117.0275 Evaluate side-chains 336 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 293 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 B residue 43 VAL Chi-restraints excluded: chain B residue 84 CYS 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 265 CYS Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 105 LEU 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 43 VAL Chi-restraints excluded: chain D residue 66 CYS 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 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 105 LEU Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 265 CYS 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 53 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12040 Z= 0.183 Angle : 0.614 7.302 16422 Z= 0.297 Chirality : 0.039 0.128 1995 Planarity : 0.004 0.037 1953 Dihedral : 3.584 17.047 1554 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.63 % Allowed : 25.02 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1407 helix: 2.00 (0.17), residues: 1001 sheet: -1.24 (0.55), residues: 84 loop : -2.12 (0.30), residues: 322 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 0.027 0.001 PHE G 126 TYR 0.021 0.001 TYR B 293 ARG 0.009 0.001 ARG A 29 *********************** 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 360 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 312 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9119 (tptt) cc_final: 0.8725 (tttt) REVERT: A 111 TYR cc_start: 0.8585 (m-10) cc_final: 0.7895 (m-10) REVERT: A 301 GLN cc_start: 0.7727 (pp30) cc_final: 0.7426 (pp30) REVERT: A 326 ASN cc_start: 0.6669 (p0) cc_final: 0.5916 (p0) REVERT: A 328 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8450 (tt) REVERT: B 36 LYS cc_start: 0.9049 (tptt) cc_final: 0.8591 (tttt) REVERT: B 75 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8428 (mmt180) REVERT: B 111 TYR cc_start: 0.8647 (m-10) cc_final: 0.7969 (m-10) REVERT: B 247 SER cc_start: 0.8378 (t) cc_final: 0.8155 (m) REVERT: B 265 CYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8260 (m) REVERT: B 301 GLN cc_start: 0.8021 (pp30) cc_final: 0.7764 (pp30) REVERT: B 326 ASN cc_start: 0.6791 (p0) cc_final: 0.6108 (p0) REVERT: C 36 LYS cc_start: 0.9110 (tptt) cc_final: 0.8766 (tttt) REVERT: C 75 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8456 (mmt180) REVERT: C 111 TYR cc_start: 0.8593 (m-10) cc_final: 0.8070 (m-10) REVERT: C 213 TYR cc_start: 0.8857 (t80) cc_final: 0.8587 (t80) REVERT: C 326 ASN cc_start: 0.6738 (p0) cc_final: 0.6183 (p0) REVERT: D 36 LYS cc_start: 0.9170 (tptt) cc_final: 0.8736 (tttt) REVERT: D 75 ARG cc_start: 0.8655 (mmm160) cc_final: 0.8279 (mmt180) REVERT: D 111 TYR cc_start: 0.8626 (m-10) cc_final: 0.8057 (m-10) REVERT: D 212 LYS cc_start: 0.8091 (mttp) cc_final: 0.7574 (mttp) REVERT: D 301 GLN cc_start: 0.7898 (pp30) cc_final: 0.7499 (pp30) REVERT: D 326 ASN cc_start: 0.6907 (p0) cc_final: 0.6074 (p0) REVERT: E 36 LYS cc_start: 0.9069 (tptt) cc_final: 0.8641 (tttt) REVERT: E 111 TYR cc_start: 0.8776 (m-10) cc_final: 0.7835 (m-10) REVERT: E 276 LEU cc_start: 0.9162 (mt) cc_final: 0.8934 (mt) REVERT: E 326 ASN cc_start: 0.6643 (p0) cc_final: 0.5980 (p0) REVERT: F 36 LYS cc_start: 0.9166 (tptt) cc_final: 0.8636 (tttt) REVERT: F 75 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8338 (mmt180) REVERT: F 111 TYR cc_start: 0.8680 (m-10) cc_final: 0.7894 (m-10) REVERT: F 326 ASN cc_start: 0.6950 (p0) cc_final: 0.6191 (p0) REVERT: G 36 LYS cc_start: 0.9097 (tptt) cc_final: 0.8683 (tttt) REVERT: G 75 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8202 (mmt180) REVERT: G 111 TYR cc_start: 0.8614 (m-10) cc_final: 0.8023 (m-10) REVERT: G 212 LYS cc_start: 0.7993 (mttp) cc_final: 0.7483 (mttp) REVERT: G 301 GLN cc_start: 0.7918 (pp30) cc_final: 0.7495 (pp30) REVERT: G 326 ASN cc_start: 0.7118 (p0) cc_final: 0.6674 (p0) REVERT: G 334 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7964 (t80) outliers start: 48 outliers final: 35 residues processed: 328 average time/residue: 0.2691 time to fit residues: 120.0024 Evaluate side-chains 331 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 293 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 84 CYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 105 LEU 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 43 VAL Chi-restraints excluded: chain D residue 66 CYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU 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 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 105 LEU Chi-restraints excluded: chain G residue 218 LEU 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 117 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12040 Z= 0.263 Angle : 0.652 7.849 16422 Z= 0.317 Chirality : 0.041 0.129 1995 Planarity : 0.004 0.035 1953 Dihedral : 3.715 17.278 1554 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.40 % Allowed : 25.85 % Favored : 70.75 % 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: 1.24 (0.23), residues: 1407 helix: 1.89 (0.17), residues: 1001 sheet: -1.16 (0.56), residues: 84 loop : -2.10 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 85 HIS 0.002 0.000 HIS E 106 PHE 0.038 0.001 PHE G 126 TYR 0.020 0.001 TYR C 230 ARG 0.006 0.001 ARG F 29 *********************** 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 330 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 285 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9103 (tptt) cc_final: 0.8723 (tttt) REVERT: A 111 TYR cc_start: 0.8659 (m-10) cc_final: 0.7953 (m-10) REVERT: A 301 GLN cc_start: 0.7761 (pp30) cc_final: 0.7533 (pp30) REVERT: A 326 ASN cc_start: 0.6843 (p0) cc_final: 0.6112 (p0) REVERT: A 328 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8432 (tt) REVERT: B 36 LYS cc_start: 0.9018 (tptt) cc_final: 0.8555 (tttt) REVERT: B 75 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8432 (mmt180) REVERT: B 111 TYR cc_start: 0.8764 (m-10) cc_final: 0.8123 (m-10) REVERT: B 265 CYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8292 (m) REVERT: B 301 GLN cc_start: 0.7962 (pp30) cc_final: 0.7745 (pp30) REVERT: B 326 ASN cc_start: 0.6936 (p0) cc_final: 0.6164 (p0) REVERT: C 36 LYS cc_start: 0.9102 (tptt) cc_final: 0.8773 (tttt) REVERT: C 111 TYR cc_start: 0.8795 (m-10) cc_final: 0.8262 (m-10) REVERT: D 36 LYS cc_start: 0.9161 (tptt) cc_final: 0.8733 (tttt) REVERT: D 75 ARG cc_start: 0.8653 (mmm160) cc_final: 0.8308 (mmt180) REVERT: D 111 TYR cc_start: 0.8756 (m-10) cc_final: 0.8009 (m-10) REVERT: D 212 LYS cc_start: 0.8141 (mttp) cc_final: 0.7614 (mttp) REVERT: D 301 GLN cc_start: 0.8034 (pp30) cc_final: 0.7652 (pp30) REVERT: D 326 ASN cc_start: 0.7099 (p0) cc_final: 0.6275 (p0) REVERT: E 36 LYS cc_start: 0.9068 (tptt) cc_final: 0.8641 (tttt) REVERT: E 111 TYR cc_start: 0.8868 (m-10) cc_final: 0.7986 (m-10) REVERT: E 326 ASN cc_start: 0.6747 (p0) cc_final: 0.6050 (p0) REVERT: F 36 LYS cc_start: 0.9164 (tptt) cc_final: 0.8636 (tttt) REVERT: F 75 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8371 (mmt180) REVERT: F 326 ASN cc_start: 0.7044 (p0) cc_final: 0.6255 (p0) REVERT: G 36 LYS cc_start: 0.9103 (tptt) cc_final: 0.8690 (tttt) REVERT: G 75 ARG cc_start: 0.8603 (mmm160) cc_final: 0.8294 (mmt180) REVERT: G 111 TYR cc_start: 0.8721 (m-10) cc_final: 0.8108 (m-10) REVERT: G 212 LYS cc_start: 0.7952 (mttp) cc_final: 0.7435 (mttp) REVERT: G 301 GLN cc_start: 0.7866 (pp30) cc_final: 0.7446 (pp30) REVERT: G 326 ASN cc_start: 0.7316 (p0) cc_final: 0.6846 (p0) REVERT: G 334 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8020 (t80) outliers start: 45 outliers final: 36 residues processed: 300 average time/residue: 0.2915 time to fit residues: 116.9799 Evaluate side-chains 317 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 278 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 84 CYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 105 LEU 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 43 VAL Chi-restraints excluded: chain D residue 66 CYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU 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 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 105 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 0.0670 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 68 optimal weight: 0.0010 chunk 88 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.5126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12040 Z= 0.166 Angle : 0.616 7.335 16422 Z= 0.297 Chirality : 0.039 0.130 1995 Planarity : 0.004 0.037 1953 Dihedral : 3.514 14.929 1554 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.80 % Allowed : 26.46 % Favored : 70.75 % 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: 1.46 (0.23), residues: 1407 helix: 2.09 (0.17), residues: 994 sheet: -0.97 (0.55), residues: 84 loop : -2.12 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 74 HIS 0.000 0.000 HIS G 134 PHE 0.035 0.001 PHE G 126 TYR 0.018 0.001 TYR B 293 ARG 0.004 0.000 ARG G 128 ********************** 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 346 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 309 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.9092 (tptt) cc_final: 0.8720 (tttt) REVERT: A 111 TYR cc_start: 0.8526 (m-10) cc_final: 0.7978 (m-10) REVERT: A 326 ASN cc_start: 0.6741 (p0) cc_final: 0.5994 (p0) REVERT: A 328 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8437 (tt) REVERT: B 29 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7212 (ptp90) REVERT: B 36 LYS cc_start: 0.9028 (tptt) cc_final: 0.8581 (tttt) REVERT: B 75 ARG cc_start: 0.8655 (mmm160) cc_final: 0.8416 (mmt180) REVERT: B 111 TYR cc_start: 0.8625 (m-10) cc_final: 0.7949 (m-10) REVERT: B 265 CYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8251 (m) REVERT: B 301 GLN cc_start: 0.8048 (pp30) cc_final: 0.7825 (pp30) REVERT: B 326 ASN cc_start: 0.6778 (p0) cc_final: 0.6110 (p0) REVERT: C 36 LYS cc_start: 0.9078 (tptt) cc_final: 0.8753 (tttt) REVERT: C 111 TYR cc_start: 0.8525 (m-10) cc_final: 0.7929 (m-10) REVERT: C 213 TYR cc_start: 0.8836 (t80) cc_final: 0.8552 (t80) REVERT: C 326 ASN cc_start: 0.6687 (p0) cc_final: 0.6111 (p0) REVERT: D 36 LYS cc_start: 0.9153 (tptt) cc_final: 0.8718 (tttt) REVERT: D 75 ARG cc_start: 0.8660 (mmm160) cc_final: 0.8288 (mmt180) REVERT: D 83 TYR cc_start: 0.8685 (t80) cc_final: 0.8431 (t80) REVERT: D 111 TYR cc_start: 0.8555 (m-10) cc_final: 0.8007 (m-10) REVERT: D 208 ASN cc_start: 0.8199 (p0) cc_final: 0.7954 (p0) REVERT: D 212 LYS cc_start: 0.8108 (mttp) cc_final: 0.7570 (mttp) REVERT: D 301 GLN cc_start: 0.7988 (pp30) cc_final: 0.7523 (pp30) REVERT: D 326 ASN cc_start: 0.6790 (p0) cc_final: 0.5971 (p0) REVERT: E 36 LYS cc_start: 0.9050 (tptt) cc_final: 0.8635 (tttt) REVERT: E 111 TYR cc_start: 0.8728 (m-10) cc_final: 0.7897 (m-10) REVERT: E 326 ASN cc_start: 0.6623 (p0) cc_final: 0.5969 (p0) REVERT: F 36 LYS cc_start: 0.9101 (tptt) cc_final: 0.8657 (tttt) REVERT: F 75 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8333 (mmt180) REVERT: F 111 TYR cc_start: 0.8679 (m-10) cc_final: 0.7898 (m-10) REVERT: F 326 ASN cc_start: 0.6825 (p0) cc_final: 0.6021 (p0) REVERT: G 36 LYS cc_start: 0.9116 (tptt) cc_final: 0.8710 (tttt) REVERT: G 75 ARG cc_start: 0.8528 (mmm160) cc_final: 0.8196 (mmt180) REVERT: G 111 TYR cc_start: 0.8546 (m-10) cc_final: 0.7982 (m-10) REVERT: G 212 LYS cc_start: 0.7991 (mttp) cc_final: 0.7784 (mttp) REVERT: G 301 GLN cc_start: 0.7763 (pp30) cc_final: 0.7424 (pp30) REVERT: G 326 ASN cc_start: 0.7092 (p0) cc_final: 0.6648 (p0) REVERT: G 334 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8011 (t80) outliers start: 37 outliers final: 31 residues processed: 318 average time/residue: 0.2673 time to fit residues: 114.9981 Evaluate side-chains 335 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 301 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 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 84 CYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 105 LEU 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 66 CYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 218 LEU 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 292 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain G residue 105 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 0.0570 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 97 optimal weight: 0.0870 chunk 6 optimal weight: 0.9980 overall best weight: 0.8278 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.116010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.090699 restraints weight = 19803.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.093017 restraints weight = 10744.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.094503 restraints weight = 7595.821| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12040 Z= 0.183 Angle : 0.631 7.549 16422 Z= 0.304 Chirality : 0.039 0.128 1995 Planarity : 0.004 0.037 1953 Dihedral : 3.497 13.795 1554 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.72 % Allowed : 26.91 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1407 helix: 1.99 (0.17), residues: 994 sheet: -0.82 (0.56), residues: 84 loop : -1.83 (0.31), residues: 329 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 0.034 0.001 PHE G 126 TYR 0.019 0.001 TYR B 293 ARG 0.004 0.000 ARG E 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2661.79 seconds wall clock time: 48 minutes 55.89 seconds (2935.89 seconds total)