Starting phenix.real_space_refine on Sun Oct 25 04:53:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t34_55483/10_2026/9t34_55483.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t34_55483/10_2026/9t34_55483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t34_55483/10_2026/9t34_55483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t34_55483/10_2026/9t34_55483.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t34_55483/10_2026/9t34_55483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t34_55483/10_2026/9t34_55483.map" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 102 5.16 5 C 10164 2.51 5 N 2436 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15342 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2557 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.83, per 1000 atoms: 0.18 Number of scatterers: 15342 At special positions: 0 Unit cell: (108.066, 102.858, 121.086, 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 102 16.00 O 2640 8.00 N 2436 7.00 C 10164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " 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: 1.22 Conformation dependent library (CDL) restraints added in 678.1 milliseconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 12 sheets defined 77.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.121A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 169 through 179 removed outlier: 3.533A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 314 through 347 removed outlier: 3.776A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.004A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 4.121A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 142 through 145 Processing helix chain 'B' and resid 146 through 165 Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.533A pdb=" N VAL B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 314 through 347 removed outlier: 3.776A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 371 through 383 Processing helix chain 'B' and resid 383 through 394 removed outlier: 4.003A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 removed outlier: 4.121A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 21 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 142 through 145 Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 169 through 179 removed outlier: 3.534A pdb=" N VAL C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 314 through 347 removed outlier: 3.776A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 371 through 383 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.003A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 4.121A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 21 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 141 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 146 through 165 Processing helix chain 'D' and resid 169 through 179 removed outlier: 3.533A pdb=" N VAL D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 314 through 347 removed outlier: 3.775A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 371 through 383 Processing helix chain 'D' and resid 383 through 394 removed outlier: 4.003A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 21 removed outlier: 4.121A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E 21 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 141 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 142 through 145 Processing helix chain 'E' and resid 146 through 165 Processing helix chain 'E' and resid 169 through 179 removed outlier: 3.534A pdb=" N VAL E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 314 through 347 removed outlier: 3.777A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 371 through 383 Processing helix chain 'E' and resid 383 through 394 removed outlier: 4.003A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 21 removed outlier: 4.121A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS F 21 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 141 Proline residue: F 126 - end of helix Processing helix chain 'F' and resid 142 through 145 Processing helix chain 'F' and resid 146 through 165 Processing helix chain 'F' and resid 169 through 179 removed outlier: 3.533A pdb=" N VAL F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 314 through 347 removed outlier: 3.776A pdb=" N SER F 347 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 371 through 383 Processing helix chain 'F' and resid 383 through 394 removed outlier: 4.003A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB1, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 60 through 61 1080 hydrogen bonds defined for protein. 3150 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: 2.50 Time building geometry restraints manager: 1.69 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: 4524 1.34 - 1.46: 4269 1.46 - 1.58: 6843 1.58 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 15780 Sorted by residual: bond pdb=" CB PRO D 15 " pdb=" CG PRO D 15 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.82e-01 bond pdb=" CB PRO B 15 " pdb=" CG PRO B 15 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.72e-01 bond pdb=" CB PRO C 15 " pdb=" CG PRO C 15 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.48e-01 bond pdb=" CB PRO E 15 " pdb=" CG PRO E 15 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.45e-01 bond pdb=" CB PRO A 15 " pdb=" CG PRO A 15 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.43e-01 ... (remaining 15775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 20880 0.97 - 1.94: 402 1.94 - 2.91: 57 2.91 - 3.88: 15 3.88 - 4.85: 12 Bond angle restraints: 21366 Sorted by residual: angle pdb=" C LYS F 369 " pdb=" N ASN F 370 " pdb=" CA ASN F 370 " ideal model delta sigma weight residual 121.81 119.12 2.69 1.83e+00 2.99e-01 2.15e+00 angle pdb=" C LYS D 369 " pdb=" N ASN D 370 " pdb=" CA ASN D 370 " ideal model delta sigma weight residual 121.81 119.14 2.67 1.83e+00 2.99e-01 2.13e+00 angle pdb=" C LYS B 369 " pdb=" N ASN B 370 " pdb=" CA ASN B 370 " ideal model delta sigma weight residual 121.81 119.16 2.65 1.83e+00 2.99e-01 2.10e+00 angle pdb=" C LYS C 369 " pdb=" N ASN C 370 " pdb=" CA ASN C 370 " ideal model delta sigma weight residual 121.81 119.18 2.63 1.83e+00 2.99e-01 2.07e+00 angle pdb=" C LYS E 369 " pdb=" N ASN E 370 " pdb=" CA ASN E 370 " ideal model delta sigma weight residual 121.81 119.18 2.63 1.83e+00 2.99e-01 2.06e+00 ... (remaining 21361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.57: 8335 10.57 - 21.14: 585 21.14 - 31.72: 218 31.72 - 42.29: 90 42.29 - 52.86: 42 Dihedral angle restraints: 9270 sinusoidal: 3786 harmonic: 5484 Sorted by residual: dihedral pdb=" CA LYS C 369 " pdb=" C LYS C 369 " pdb=" N ASN C 370 " pdb=" CA ASN C 370 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LYS E 369 " pdb=" C LYS E 369 " pdb=" N ASN E 370 " pdb=" CA ASN E 370 " ideal model delta harmonic sigma weight residual -180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LYS B 369 " pdb=" C LYS B 369 " pdb=" N ASN B 370 " pdb=" CA ASN B 370 " ideal model delta harmonic sigma weight residual -180.00 -161.69 -18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 9267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1360 0.025 - 0.050: 597 0.050 - 0.075: 302 0.075 - 0.100: 54 0.100 - 0.125: 45 Chirality restraints: 2358 Sorted by residual: chirality pdb=" CA ILE F 53 " pdb=" N ILE F 53 " pdb=" C ILE F 53 " pdb=" CB ILE F 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE A 53 " pdb=" N ILE A 53 " pdb=" C ILE A 53 " pdb=" CB ILE A 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE E 53 " pdb=" N ILE E 53 " pdb=" C ILE E 53 " pdb=" CB ILE E 53 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 2355 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 21 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO F 22 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO F 22 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 22 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 21 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO B 22 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 22 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 22 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 21 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO A 22 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " -0.014 5.00e-02 4.00e+02 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.11: 11680 3.11 - 3.56: 16905 3.56 - 4.00: 22963 4.00 - 4.45: 28908 4.45 - 4.90: 42742 Nonbonded interactions: 123198 Sorted by model distance: nonbonded pdb=" C ASP E 110 " pdb=" CG ASP E 110 " model vdw 2.662 2.800 nonbonded pdb=" C ASP B 110 " pdb=" CG ASP B 110 " model vdw 2.663 2.800 nonbonded pdb=" C ASP A 110 " pdb=" CG ASP A 110 " model vdw 2.663 2.800 nonbonded pdb=" C ASP C 110 " pdb=" CG ASP C 110 " model vdw 2.663 2.800 nonbonded pdb=" C ASP F 110 " pdb=" CG ASP F 110 " model vdw 2.663 2.800 ... (remaining 123193 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 : 0.002 0.038 15798 Z= 0.098 Angle : 0.360 4.851 21402 Z= 0.194 Chirality : 0.036 0.125 2358 Planarity : 0.002 0.026 2568 Dihedral : 9.795 52.862 5664 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.18 % Allowed : 7.83 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.71 (0.19), residues: 1782 helix: 3.17 (0.13), residues: 1224 sheet: 3.42 (0.48), residues: 96 loop : 0.17 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 262 TYR 0.008 0.001 TYR B 281 PHE 0.006 0.001 PHE F 275 TRP 0.010 0.001 TRP C 24 HIS 0.002 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (15780) covalent geometry : angle 0.36002 / 0.19 (21366) SS BOND : bond 0.00135 / 0.09 ( 18) SS BOND : angle 0.45224 / 0.30 ( 36) hydrogen bonds : bond 0.13047 / 8.70 ( 1080) hydrogen bonds : angle 5.34409 / 3.83 ( 3150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 307 time to evaluate : 0.602 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: A 37 MET cc_start: 0.9456 (ttp) cc_final: 0.9197 (ttp) REVERT: A 51 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8135 (mtmt) REVERT: A 249 LYS cc_start: 0.9619 (mtpt) cc_final: 0.9382 (mmtm) REVERT: A 330 ILE cc_start: 0.9446 (mt) cc_final: 0.9235 (mp) REVERT: B 35 MET cc_start: 0.9252 (mtp) cc_final: 0.9018 (mtm) REVERT: B 37 MET cc_start: 0.9368 (ttp) cc_final: 0.8680 (tmm) REVERT: B 164 PHE cc_start: 0.9402 (t80) cc_final: 0.9033 (t80) REVERT: B 274 LYS cc_start: 0.8602 (tptt) cc_final: 0.8394 (tptp) REVERT: C 37 MET cc_start: 0.9453 (ttp) cc_final: 0.9172 (ttp) REVERT: C 243 LEU cc_start: 0.9328 (tp) cc_final: 0.9070 (tp) REVERT: C 248 LYS cc_start: 0.9449 (tttp) cc_final: 0.9248 (tppt) REVERT: C 249 LYS cc_start: 0.9642 (mtpt) cc_final: 0.9403 (mmmt) REVERT: D 51 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8119 (mtmt) REVERT: D 52 MET cc_start: 0.8690 (tpt) cc_final: 0.8478 (mmm) REVERT: D 239 GLN cc_start: 0.9042 (mt0) cc_final: 0.8826 (tp40) REVERT: D 243 LEU cc_start: 0.9312 (tp) cc_final: 0.9030 (tp) REVERT: D 249 LYS cc_start: 0.9640 (mtpt) cc_final: 0.9429 (mmmt) REVERT: D 317 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9359 (tp) REVERT: D 324 PHE cc_start: 0.9173 (t80) cc_final: 0.8648 (m-80) REVERT: E 153 LEU cc_start: 0.9473 (mt) cc_final: 0.9252 (mt) REVERT: F 249 LYS cc_start: 0.9676 (mtpt) cc_final: 0.9406 (mmmt) REVERT: F 330 ILE cc_start: 0.9511 (mt) cc_final: 0.9237 (mp) REVERT: F 375 MET cc_start: 0.8816 (mtm) cc_final: 0.8380 (mtm) outliers start: 54 outliers final: 16 residues processed: 349 average time/residue: 0.1292 time to fit residues: 65.9222 Evaluate side-chains 176 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 275 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 GLN B 105 GLN C 105 GLN D 105 GLN D 239 GLN E 105 GLN F 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.063424 restraints weight = 38381.720| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.22 r_work: 0.2752 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15798 Z= 0.183 Angle : 0.491 5.513 21402 Z= 0.269 Chirality : 0.041 0.212 2358 Planarity : 0.003 0.038 2568 Dihedral : 5.699 49.664 2062 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.42 % Allowed : 12.49 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.62 (0.19), residues: 1782 helix: 2.99 (0.13), residues: 1260 sheet: 3.41 (0.45), residues: 96 loop : 0.21 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 171 TYR 0.017 0.001 TYR A 261 PHE 0.012 0.001 PHE E 164 TRP 0.018 0.001 TRP B 168 HIS 0.003 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (15780) covalent geometry : angle 0.49070 / 0.27 (21366) SS BOND : bond 0.00312 / 0.19 ( 18) SS BOND : angle 0.83507 / 0.49 ( 36) hydrogen bonds : bond 0.03997 / 2.68 ( 1080) hydrogen bonds : angle 4.19560 / 3.00 ( 3150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8938 (t0) cc_final: 0.8678 (t0) REVERT: A 37 MET cc_start: 0.9420 (ttp) cc_final: 0.9211 (mtp) REVERT: A 51 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7962 (mtmt) REVERT: A 52 MET cc_start: 0.8779 (mmm) cc_final: 0.7737 (mmm) REVERT: A 274 LYS cc_start: 0.8788 (tppt) cc_final: 0.8564 (tppt) REVERT: A 325 TYR cc_start: 0.9152 (t80) cc_final: 0.8947 (t80) REVERT: A 330 ILE cc_start: 0.9334 (mt) cc_final: 0.9117 (mp) REVERT: B 160 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8847 (tt) REVERT: B 278 ILE cc_start: 0.8781 (pt) cc_final: 0.8353 (mt) REVERT: C 98 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9139 (mttp) REVERT: C 249 LYS cc_start: 0.9650 (mtpt) cc_final: 0.9348 (mmmt) REVERT: D 51 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7903 (mtmt) REVERT: D 52 MET cc_start: 0.8623 (tpt) cc_final: 0.8296 (mmm) REVERT: D 53 ILE cc_start: 0.9144 (mt) cc_final: 0.8873 (mm) REVERT: D 239 GLN cc_start: 0.9098 (mt0) cc_final: 0.8836 (tp40) REVERT: D 243 LEU cc_start: 0.9288 (tp) cc_final: 0.9045 (tp) REVERT: D 249 LYS cc_start: 0.9603 (mtpt) cc_final: 0.9316 (mmtm) REVERT: D 276 ILE cc_start: 0.9356 (tt) cc_final: 0.9141 (tp) REVERT: D 324 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8701 (m-80) REVERT: E 160 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9037 (tt) REVERT: E 171 ARG cc_start: 0.8891 (ptm160) cc_final: 0.8670 (ptm160) REVERT: E 325 TYR cc_start: 0.9199 (t80) cc_final: 0.8983 (t80) REVERT: F 249 LYS cc_start: 0.9669 (mtpt) cc_final: 0.9391 (mmmt) REVERT: F 265 MET cc_start: 0.9017 (ttm) cc_final: 0.8815 (ttp) REVERT: F 375 MET cc_start: 0.8911 (mtm) cc_final: 0.8386 (mtm) outliers start: 58 outliers final: 36 residues processed: 230 average time/residue: 0.1324 time to fit residues: 44.3602 Evaluate side-chains 195 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain D residue 51 LYS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 392 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [145, 20, 143, 124, 6, 138, 56, 59, 92, 112, 136] chunk 145 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 267 GLN F 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.065017 restraints weight = 38594.456| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.27 r_work: 0.2796 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15798 Z= 0.111 Angle : 0.434 5.727 21402 Z= 0.238 Chirality : 0.039 0.204 2358 Planarity : 0.003 0.043 2568 Dihedral : 5.377 49.220 2056 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.47 % Allowed : 13.31 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.19), residues: 1782 helix: 2.98 (0.13), residues: 1260 sheet: 3.72 (0.43), residues: 96 loop : 0.19 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 171 TYR 0.020 0.001 TYR D 325 PHE 0.015 0.001 PHE D 393 TRP 0.023 0.001 TRP B 168 HIS 0.002 0.001 HIS F 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15780) covalent geometry : angle 0.43431 / 0.24 (21366) SS BOND : bond 0.00212 / 0.14 ( 18) SS BOND : angle 0.52448 / 0.32 ( 36) hydrogen bonds : bond 0.03490 / 2.35 ( 1080) hydrogen bonds : angle 3.92863 / 2.81 ( 3150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 LYS cc_start: 0.9605 (mtpt) cc_final: 0.9391 (mmtm) REVERT: B 160 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8819 (tt) REVERT: B 164 PHE cc_start: 0.9420 (t80) cc_final: 0.8855 (t80) REVERT: B 278 ILE cc_start: 0.8736 (pt) cc_final: 0.8412 (mt) REVERT: C 29 ASP cc_start: 0.9052 (m-30) cc_final: 0.8633 (t0) REVERT: C 236 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9159 (mp0) REVERT: C 249 LYS cc_start: 0.9647 (mtpt) cc_final: 0.9356 (mmmt) REVERT: D 243 LEU cc_start: 0.9332 (tp) cc_final: 0.9110 (tp) REVERT: D 249 LYS cc_start: 0.9605 (mtpt) cc_final: 0.9325 (mmtm) REVERT: D 324 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8731 (m-80) REVERT: E 160 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9006 (tt) REVERT: E 168 TRP cc_start: 0.8728 (m-90) cc_final: 0.8301 (m-90) REVERT: F 52 MET cc_start: 0.8824 (mmm) cc_final: 0.8341 (ttm) REVERT: F 249 LYS cc_start: 0.9662 (mtpt) cc_final: 0.9384 (mmmt) REVERT: F 343 MET cc_start: 0.8992 (mtp) cc_final: 0.8786 (ttm) REVERT: F 375 MET cc_start: 0.8837 (mtm) cc_final: 0.8273 (mtm) outliers start: 59 outliers final: 40 residues processed: 224 average time/residue: 0.1178 time to fit residues: 39.1517 Evaluate side-chains 190 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 392 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [109, 141, 149, 165, 162, 44, 30, 62, 21, 65, 114] chunk 109 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.064343 restraints weight = 38977.912| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.28 r_work: 0.2780 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15798 Z= 0.125 Angle : 0.450 8.472 21402 Z= 0.243 Chirality : 0.039 0.243 2358 Planarity : 0.003 0.046 2568 Dihedral : 5.349 50.118 2048 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.36 % Allowed : 14.08 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.64 (0.19), residues: 1782 helix: 2.99 (0.13), residues: 1260 sheet: 3.90 (0.41), residues: 96 loop : 0.15 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 171 TYR 0.030 0.001 TYR E 325 PHE 0.012 0.001 PHE D 393 TRP 0.019 0.001 TRP A 168 HIS 0.002 0.001 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15780) covalent geometry : angle 0.44953 / 0.24 (21366) SS BOND : bond 0.00243 / 0.15 ( 18) SS BOND : angle 0.50871 / 0.30 ( 36) hydrogen bonds : bond 0.03474 / 2.35 ( 1080) hydrogen bonds : angle 3.87730 / 2.77 ( 3150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8921 (t0) cc_final: 0.8696 (t0) REVERT: A 52 MET cc_start: 0.8009 (ttm) cc_final: 0.7543 (ttm) REVERT: A 274 LYS cc_start: 0.8871 (tppt) cc_final: 0.8668 (tppt) REVERT: B 160 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8895 (tt) REVERT: B 164 PHE cc_start: 0.9408 (t80) cc_final: 0.8868 (t80) REVERT: B 278 ILE cc_start: 0.8586 (pt) cc_final: 0.8291 (mt) REVERT: C 249 LYS cc_start: 0.9638 (mtpt) cc_final: 0.9334 (mmmt) REVERT: D 243 LEU cc_start: 0.9348 (tp) cc_final: 0.9113 (tp) REVERT: D 265 MET cc_start: 0.8933 (ttp) cc_final: 0.8694 (ttp) REVERT: D 324 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8730 (m-80) REVERT: E 52 MET cc_start: 0.8622 (ttm) cc_final: 0.8187 (ttm) REVERT: E 160 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9003 (tt) REVERT: E 168 TRP cc_start: 0.8743 (m-90) cc_final: 0.8274 (m-90) REVERT: F 52 MET cc_start: 0.8747 (mmm) cc_final: 0.8301 (ttm) REVERT: F 163 CYS cc_start: 0.9270 (m) cc_final: 0.8951 (t) REVERT: F 249 LYS cc_start: 0.9642 (mtpt) cc_final: 0.9348 (mmmt) REVERT: F 375 MET cc_start: 0.8860 (mtm) cc_final: 0.8305 (mtm) outliers start: 57 outliers final: 39 residues processed: 211 average time/residue: 0.1164 time to fit residues: 37.0200 Evaluate side-chains 186 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [121, 19, 33, 127, 13, 73, 0, 165, 133, 24, 178] chunk 121 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.065119 restraints weight = 39137.485| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.27 r_work: 0.2789 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15798 Z= 0.116 Angle : 0.452 7.224 21402 Z= 0.243 Chirality : 0.039 0.282 2358 Planarity : 0.003 0.050 2568 Dihedral : 5.261 50.358 2044 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.36 % Allowed : 14.08 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.19), residues: 1782 helix: 2.99 (0.13), residues: 1260 sheet: 3.90 (0.40), residues: 96 loop : 0.17 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 171 TYR 0.031 0.001 TYR E 325 PHE 0.015 0.001 PHE D 393 TRP 0.022 0.001 TRP A 168 HIS 0.012 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (15780) covalent geometry : angle 0.45167 / 0.24 (21366) SS BOND : bond 0.00199 / 0.12 ( 18) SS BOND : angle 0.41852 / 0.25 ( 36) hydrogen bonds : bond 0.03377 / 2.29 ( 1080) hydrogen bonds : angle 3.83115 / 2.74 ( 3150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.7940 (ttm) cc_final: 0.7452 (ttm) REVERT: A 343 MET cc_start: 0.9234 (ttp) cc_final: 0.8932 (ttp) REVERT: B 52 MET cc_start: 0.8828 (ttt) cc_final: 0.7969 (ttm) REVERT: B 164 PHE cc_start: 0.9410 (t80) cc_final: 0.8924 (t80) REVERT: B 278 ILE cc_start: 0.8612 (pt) cc_final: 0.8391 (mt) REVERT: D 243 LEU cc_start: 0.9349 (tp) cc_final: 0.9075 (tp) REVERT: D 324 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8738 (m-80) REVERT: E 52 MET cc_start: 0.8628 (ttm) cc_final: 0.8178 (ttm) REVERT: E 160 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8984 (tt) REVERT: E 168 TRP cc_start: 0.8790 (m-90) cc_final: 0.8440 (m-90) REVERT: E 265 MET cc_start: 0.9007 (tpp) cc_final: 0.8633 (tpp) REVERT: F 52 MET cc_start: 0.8721 (mmm) cc_final: 0.8403 (ttm) REVERT: F 249 LYS cc_start: 0.9637 (mtpt) cc_final: 0.9351 (mmmt) REVERT: F 375 MET cc_start: 0.8859 (mtm) cc_final: 0.8273 (mtm) outliers start: 57 outliers final: 37 residues processed: 215 average time/residue: 0.1123 time to fit residues: 36.8934 Evaluate side-chains 184 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [74, 149, 122, 47, 45, 37, 83, 134, 69, 24, 99] chunk 74 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS D 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.064796 restraints weight = 38827.879| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.23 r_work: 0.2790 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15798 Z= 0.111 Angle : 0.453 6.688 21402 Z= 0.244 Chirality : 0.039 0.284 2358 Planarity : 0.003 0.049 2568 Dihedral : 5.272 50.415 2044 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.53 % Allowed : 14.78 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.19), residues: 1782 helix: 3.00 (0.13), residues: 1260 sheet: 3.86 (0.40), residues: 96 loop : 0.17 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 171 TYR 0.033 0.001 TYR E 325 PHE 0.007 0.001 PHE A 156 TRP 0.026 0.001 TRP F 168 HIS 0.007 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (15780) covalent geometry : angle 0.45279 / 0.24 (21366) SS BOND : bond 0.00184 / 0.11 ( 18) SS BOND : angle 0.39545 / 0.24 ( 36) hydrogen bonds : bond 0.03289 / 2.22 ( 1080) hydrogen bonds : angle 3.77911 / 2.71 ( 3150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8892 (t0) cc_final: 0.8690 (t0) REVERT: A 52 MET cc_start: 0.7957 (ttm) cc_final: 0.7463 (ttm) REVERT: A 265 MET cc_start: 0.9160 (tpp) cc_final: 0.8907 (tpp) REVERT: A 377 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7788 (m170) REVERT: B 52 MET cc_start: 0.8721 (ttt) cc_final: 0.8496 (ttm) REVERT: B 164 PHE cc_start: 0.9415 (t80) cc_final: 0.8963 (t80) REVERT: B 236 GLU cc_start: 0.9437 (mp0) cc_final: 0.9198 (mp0) REVERT: B 278 ILE cc_start: 0.8601 (pt) cc_final: 0.8393 (mt) REVERT: C 164 PHE cc_start: 0.9369 (t80) cc_final: 0.9095 (t80) REVERT: D 243 LEU cc_start: 0.9310 (tp) cc_final: 0.9036 (tp) REVERT: D 324 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: E 52 MET cc_start: 0.8602 (ttm) cc_final: 0.8151 (ttm) REVERT: E 160 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8984 (tt) REVERT: E 168 TRP cc_start: 0.8797 (m-90) cc_final: 0.8419 (m-90) REVERT: E 265 MET cc_start: 0.8948 (tpp) cc_final: 0.8479 (tpp) REVERT: F 52 MET cc_start: 0.8697 (mmm) cc_final: 0.8447 (ttm) REVERT: F 375 MET cc_start: 0.8852 (mtm) cc_final: 0.8254 (mtm) outliers start: 43 outliers final: 33 residues processed: 191 average time/residue: 0.1092 time to fit residues: 31.8385 Evaluate side-chains 175 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [34, 178, 127, 165, 63, 65, 0, 9, 132, 47, 83] chunk 34 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 47 optimal weight: 0.1980 chunk 83 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.065924 restraints weight = 38844.989| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.25 r_work: 0.2819 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15798 Z= 0.098 Angle : 0.452 7.462 21402 Z= 0.241 Chirality : 0.039 0.305 2358 Planarity : 0.003 0.049 2568 Dihedral : 5.121 50.550 2042 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.59 % Allowed : 14.66 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.69 (0.19), residues: 1782 helix: 3.02 (0.13), residues: 1260 sheet: 3.83 (0.39), residues: 96 loop : 0.23 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 171 TYR 0.035 0.001 TYR E 325 PHE 0.007 0.001 PHE D 156 TRP 0.021 0.001 TRP F 168 HIS 0.005 0.001 HIS C 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (15780) covalent geometry : angle 0.45179 / 0.24 (21366) SS BOND : bond 0.00161 / 0.10 ( 18) SS BOND : angle 0.32840 / 0.20 ( 36) hydrogen bonds : bond 0.03135 / 2.12 ( 1080) hydrogen bonds : angle 3.75783 / 2.69 ( 3150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8228 (ttm) cc_final: 0.7779 (ttm) REVERT: A 236 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8826 (mp0) REVERT: A 265 MET cc_start: 0.9077 (tpp) cc_final: 0.8650 (mmm) REVERT: A 278 ILE cc_start: 0.8889 (pt) cc_final: 0.8527 (mt) REVERT: B 46 GLN cc_start: 0.9308 (tp40) cc_final: 0.8711 (tt0) REVERT: B 52 MET cc_start: 0.8646 (ttt) cc_final: 0.8120 (ttm) REVERT: B 236 GLU cc_start: 0.9421 (mp0) cc_final: 0.9139 (mp0) REVERT: B 278 ILE cc_start: 0.8557 (pt) cc_final: 0.8296 (mt) REVERT: C 164 PHE cc_start: 0.9322 (t80) cc_final: 0.9109 (t80) REVERT: D 49 GLN cc_start: 0.9211 (mm110) cc_final: 0.9006 (mm-40) REVERT: D 243 LEU cc_start: 0.9293 (tp) cc_final: 0.9024 (tp) REVERT: D 324 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: E 160 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9039 (tt) REVERT: E 168 TRP cc_start: 0.8654 (m-90) cc_final: 0.8451 (m-90) REVERT: E 265 MET cc_start: 0.8878 (tpp) cc_final: 0.8604 (tpp) REVERT: F 52 MET cc_start: 0.8656 (mmm) cc_final: 0.8389 (ttm) REVERT: F 249 LYS cc_start: 0.9630 (mtpt) cc_final: 0.9376 (mmmt) REVERT: F 375 MET cc_start: 0.8831 (mtm) cc_final: 0.8314 (mtm) outliers start: 44 outliers final: 37 residues processed: 198 average time/residue: 0.1179 time to fit residues: 35.2258 Evaluate side-chains 187 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [57, 114, 71, 53, 162, 138, 111, 135, 106, 116, 171] chunk 57 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.062879 restraints weight = 39463.753| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.25 r_work: 0.2748 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15798 Z= 0.161 Angle : 0.494 7.088 21402 Z= 0.266 Chirality : 0.040 0.259 2358 Planarity : 0.003 0.048 2568 Dihedral : 5.295 51.618 2042 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.83 % Allowed : 14.72 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.59 (0.19), residues: 1782 helix: 2.95 (0.14), residues: 1260 sheet: 3.87 (0.37), residues: 96 loop : 0.15 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 171 TYR 0.038 0.001 TYR B 325 PHE 0.008 0.001 PHE C 146 TRP 0.020 0.001 TRP F 168 HIS 0.008 0.001 HIS C 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15780) covalent geometry : angle 0.49390 / 0.27 (21366) SS BOND : bond 0.00271 / 0.16 ( 18) SS BOND : angle 0.55420 / 0.34 ( 36) hydrogen bonds : bond 0.03596 / 2.41 ( 1080) hydrogen bonds : angle 3.87355 / 2.78 ( 3150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8067 (ttm) cc_final: 0.7524 (ttm) REVERT: A 265 MET cc_start: 0.8939 (tpp) cc_final: 0.8711 (tpp) REVERT: A 278 ILE cc_start: 0.8903 (pt) cc_final: 0.8545 (mt) REVERT: A 377 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.7850 (m170) REVERT: B 52 MET cc_start: 0.8496 (ttt) cc_final: 0.8240 (ttm) REVERT: B 236 GLU cc_start: 0.9248 (mp0) cc_final: 0.8942 (mp0) REVERT: C 164 PHE cc_start: 0.9366 (t80) cc_final: 0.9155 (t80) REVERT: D 49 GLN cc_start: 0.9267 (mm110) cc_final: 0.9046 (mm-40) REVERT: D 243 LEU cc_start: 0.9330 (tp) cc_final: 0.9053 (tp) REVERT: D 324 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8965 (m-80) REVERT: E 168 TRP cc_start: 0.8744 (m-90) cc_final: 0.8336 (m-90) REVERT: F 52 MET cc_start: 0.8757 (mmm) cc_final: 0.8452 (ttm) REVERT: F 375 MET cc_start: 0.8911 (mtm) cc_final: 0.8328 (mtm) outliers start: 48 outliers final: 36 residues processed: 189 average time/residue: 0.1072 time to fit residues: 31.3784 Evaluate side-chains 175 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [158, 121, 119, 124, 173, 63, 26, 100, 27, 147, 92] chunk 158 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 100 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 147 optimal weight: 0.0770 chunk 92 optimal weight: 0.9980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.065634 restraints weight = 38881.146| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.24 r_work: 0.2813 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 15798 Z= 0.103 Angle : 0.461 7.350 21402 Z= 0.246 Chirality : 0.039 0.259 2358 Planarity : 0.003 0.049 2568 Dihedral : 5.165 51.357 2042 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.00 % Allowed : 15.25 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.19), residues: 1782 helix: 2.98 (0.14), residues: 1260 sheet: 3.86 (0.37), residues: 96 loop : 0.28 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 171 TYR 0.039 0.001 TYR B 325 PHE 0.008 0.001 PHE D 156 TRP 0.020 0.001 TRP F 168 HIS 0.017 0.001 HIS F 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (15780) covalent geometry : angle 0.46113 / 0.25 (21366) SS BOND : bond 0.00158 / 0.09 ( 18) SS BOND : angle 0.35148 / 0.21 ( 36) hydrogen bonds : bond 0.03229 / 2.17 ( 1080) hydrogen bonds : angle 3.79954 / 2.73 ( 3150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8002 (ttm) cc_final: 0.7485 (ttm) REVERT: A 265 MET cc_start: 0.8940 (tpp) cc_final: 0.8695 (tpp) REVERT: B 52 MET cc_start: 0.8274 (ttt) cc_final: 0.7943 (ttm) REVERT: B 236 GLU cc_start: 0.9235 (mp0) cc_final: 0.8977 (mp0) REVERT: D 49 GLN cc_start: 0.9265 (mm110) cc_final: 0.9051 (mm-40) REVERT: D 243 LEU cc_start: 0.9294 (tp) cc_final: 0.9033 (tp) REVERT: E 265 MET cc_start: 0.8854 (tpp) cc_final: 0.8417 (tpp) REVERT: E 327 SER cc_start: 0.9357 (t) cc_final: 0.9115 (p) REVERT: F 52 MET cc_start: 0.8681 (mmm) cc_final: 0.8406 (ttm) REVERT: F 375 MET cc_start: 0.8839 (mtm) cc_final: 0.8320 (mtm) outliers start: 34 outliers final: 31 residues processed: 185 average time/residue: 0.1154 time to fit residues: 32.7917 Evaluate side-chains 170 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [144, 26, 33, 11, 50, 125, 35, 135, 116, 38, 62] chunk 144 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 33 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.082713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.065797 restraints weight = 39034.964| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.28 r_work: 0.2813 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 15798 Z= 0.105 Angle : 0.475 7.959 21402 Z= 0.251 Chirality : 0.039 0.340 2358 Planarity : 0.003 0.050 2568 Dihedral : 5.183 51.694 2042 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.94 % Allowed : 15.31 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.64 (0.19), residues: 1782 helix: 2.96 (0.13), residues: 1260 sheet: 3.91 (0.38), residues: 96 loop : 0.26 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 171 TYR 0.036 0.001 TYR E 325 PHE 0.008 0.001 PHE E 275 TRP 0.032 0.001 TRP E 168 HIS 0.013 0.001 HIS F 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (15780) covalent geometry : angle 0.47506 / 0.25 (21366) SS BOND : bond 0.00171 / 0.10 ( 18) SS BOND : angle 0.37292 / 0.22 ( 36) hydrogen bonds : bond 0.03220 / 2.17 ( 1080) hydrogen bonds : angle 3.77530 / 2.71 ( 3150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8941 (mm110) REVERT: A 52 MET cc_start: 0.8225 (ttm) cc_final: 0.7765 (ttm) REVERT: A 265 MET cc_start: 0.8913 (tpp) cc_final: 0.8691 (tpp) REVERT: A 278 ILE cc_start: 0.8898 (pt) cc_final: 0.8484 (mt) REVERT: A 377 HIS cc_start: 0.8343 (OUTLIER) cc_final: 0.7706 (m170) REVERT: B 52 MET cc_start: 0.8231 (ttt) cc_final: 0.7903 (ttm) REVERT: B 236 GLU cc_start: 0.9224 (mp0) cc_final: 0.8960 (mp0) REVERT: D 49 GLN cc_start: 0.9269 (mm110) cc_final: 0.9051 (mm-40) REVERT: D 243 LEU cc_start: 0.9314 (tp) cc_final: 0.8974 (tp) REVERT: E 265 MET cc_start: 0.8864 (tpp) cc_final: 0.8428 (tpp) REVERT: E 327 SER cc_start: 0.9378 (t) cc_final: 0.9146 (p) REVERT: E 331 PHE cc_start: 0.8754 (t80) cc_final: 0.8406 (t80) REVERT: F 52 MET cc_start: 0.8678 (mmm) cc_final: 0.8410 (ttm) outliers start: 33 outliers final: 32 residues processed: 183 average time/residue: 0.1070 time to fit residues: 30.6862 Evaluate side-chains 176 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [15, 94, 35, 125, 33, 152, 166, 148, 164, 100, 60] chunk 15 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 164 optimal weight: 0.1980 chunk 100 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.065517 restraints weight = 38845.627| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.25 r_work: 0.2812 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15798 Z= 0.112 Angle : 0.473 7.439 21402 Z= 0.253 Chirality : 0.039 0.325 2358 Planarity : 0.003 0.047 2568 Dihedral : 5.205 52.557 2042 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.00 % Allowed : 15.37 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.62 (0.19), residues: 1782 helix: 2.95 (0.14), residues: 1260 sheet: 3.79 (0.39), residues: 96 loop : 0.26 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 171 TYR 0.042 0.001 TYR B 325 PHE 0.012 0.001 PHE E 275 TRP 0.022 0.001 TRP E 168 HIS 0.013 0.001 HIS F 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (15780) covalent geometry : angle 0.47288 / 0.25 (21366) SS BOND : bond 0.00185 / 0.11 ( 18) SS BOND : angle 0.40090 / 0.24 ( 36) hydrogen bonds : bond 0.03255 / 2.19 ( 1080) hydrogen bonds : angle 3.78465 / 2.72 ( 3150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2609.99 seconds wall clock time: 45 minutes 58.68 seconds (2758.68 seconds total)