Starting phenix.real_space_refine on Wed Feb 4 22:09:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nwj_49883/02_2026/9nwj_49883.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nwj_49883/02_2026/9nwj_49883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nwj_49883/02_2026/9nwj_49883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nwj_49883/02_2026/9nwj_49883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nwj_49883/02_2026/9nwj_49883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nwj_49883/02_2026/9nwj_49883.map" } resolution = 2.69 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8636 2.51 5 N 2076 2.21 5 O 2292 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13040 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "D" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 139 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 139 Unusual residues: {'6OU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-1': 1, '6OU:plan-2': 1, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 15 Restraints were copied for chains: B, C Time building chain proxies: 3.12, per 1000 atoms: 0.24 Number of scatterers: 13040 At special positions: 0 Unit cell: (98.4713, 98.4713, 118.486, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2292 8.00 N 2076 7.00 C 8636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 153 " distance=0.00 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 387 " distance=0.00 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: 1.08 Conformation dependent library (CDL) restraints added in 496.2 milliseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 70.7% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 11 through 36 Proline residue: A 31 - end of helix removed outlier: 3.553A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 43 through 61 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.669A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.839A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 159 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 223 Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 298 removed outlier: 6.056A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.091A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 415 removed outlier: 4.464A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 36 Proline residue: B 31 - end of helix removed outlier: 3.553A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 43 through 61 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.670A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.839A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 159 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 223 Processing helix chain 'B' and resid 226 through 246 Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 280 through 298 removed outlier: 6.056A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 368 through 373 removed outlier: 4.091A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 415 removed outlier: 4.464A pdb=" N GLN B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 36 Proline residue: C 31 - end of helix removed outlier: 3.553A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'C' and resid 43 through 61 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.669A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.839A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 159 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 223 Processing helix chain 'C' and resid 226 through 246 Processing helix chain 'C' and resid 251 through 268 Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 280 through 298 removed outlier: 6.056A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.091A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 415 removed outlier: 4.464A pdb=" N GLN C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 415 " --> pdb=" O ILE C 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 36 Proline residue: D 31 - end of helix removed outlier: 3.553A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'D' and resid 43 through 61 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.670A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 98 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.839A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 159 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 223 Processing helix chain 'D' and resid 226 through 246 Processing helix chain 'D' and resid 251 through 268 Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 280 through 298 removed outlier: 6.056A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.091A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 415 removed outlier: 4.465A pdb=" N GLN D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D 415 " --> pdb=" O ILE D 411 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.541A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 322 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.540A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 322 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.541A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 322 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.541A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2364 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: 2.14 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2184 1.32 - 1.44: 3188 1.44 - 1.57: 7860 1.57 - 1.69: 24 1.69 - 1.81: 48 Bond restraints: 13304 Sorted by residual: bond pdb=" CA SER B 38 " pdb=" CB SER B 38 " ideal model delta sigma weight residual 1.527 1.476 0.051 1.15e-02 7.56e+03 1.98e+01 bond pdb=" CA SER D 38 " pdb=" CB SER D 38 " ideal model delta sigma weight residual 1.527 1.476 0.051 1.15e-02 7.56e+03 1.97e+01 bond pdb=" CA SER A 38 " pdb=" CB SER A 38 " ideal model delta sigma weight residual 1.527 1.476 0.051 1.15e-02 7.56e+03 1.97e+01 bond pdb=" CA SER C 38 " pdb=" CB SER C 38 " ideal model delta sigma weight residual 1.527 1.476 0.050 1.15e-02 7.56e+03 1.91e+01 bond pdb=" N ILE B 28 " pdb=" CA ILE B 28 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.09e-02 8.42e+03 1.25e+01 ... (remaining 13299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 15884 1.73 - 3.45: 1706 3.45 - 5.18: 304 5.18 - 6.90: 58 6.90 - 8.63: 24 Bond angle restraints: 17976 Sorted by residual: angle pdb=" N GLN D 253 " pdb=" CA GLN D 253 " pdb=" C GLN D 253 " ideal model delta sigma weight residual 113.19 107.21 5.98 1.19e+00 7.06e-01 2.53e+01 angle pdb=" N GLN A 253 " pdb=" CA GLN A 253 " pdb=" C GLN A 253 " ideal model delta sigma weight residual 113.19 107.24 5.95 1.19e+00 7.06e-01 2.50e+01 angle pdb=" N GLN B 253 " pdb=" CA GLN B 253 " pdb=" C GLN B 253 " ideal model delta sigma weight residual 113.19 107.26 5.93 1.19e+00 7.06e-01 2.48e+01 angle pdb=" N GLN C 253 " pdb=" CA GLN C 253 " pdb=" C GLN C 253 " ideal model delta sigma weight residual 113.19 107.27 5.92 1.19e+00 7.06e-01 2.47e+01 angle pdb=" N ARG C 255 " pdb=" CA ARG C 255 " pdb=" C ARG C 255 " ideal model delta sigma weight residual 112.54 106.63 5.91 1.22e+00 6.72e-01 2.35e+01 ... (remaining 17971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 7933 33.14 - 66.27: 147 66.27 - 99.41: 48 99.41 - 132.54: 24 132.54 - 165.68: 16 Dihedral angle restraints: 8168 sinusoidal: 3556 harmonic: 4612 Sorted by residual: dihedral pdb=" C34 6OU B 502 " pdb=" C31 6OU B 502 " pdb=" C33 6OU B 502 " pdb=" O30 6OU B 502 " ideal model delta sinusoidal sigma weight residual -179.71 -14.03 -165.68 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C34 6OU A 502 " pdb=" C31 6OU A 502 " pdb=" C33 6OU A 502 " pdb=" O30 6OU A 502 " ideal model delta sinusoidal sigma weight residual -179.71 -14.04 -165.67 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C34 6OU C 502 " pdb=" C31 6OU C 502 " pdb=" C33 6OU C 502 " pdb=" O30 6OU C 502 " ideal model delta sinusoidal sigma weight residual -179.71 -14.04 -165.67 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 8165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1128 0.047 - 0.093: 662 0.093 - 0.140: 210 0.140 - 0.186: 68 0.186 - 0.233: 16 Chirality restraints: 2084 Sorted by residual: chirality pdb=" CA ASP D 388 " pdb=" N ASP D 388 " pdb=" C ASP D 388 " pdb=" CB ASP D 388 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ASP A 388 " pdb=" N ASP A 388 " pdb=" C ASP A 388 " pdb=" CB ASP A 388 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP C 388 " pdb=" N ASP C 388 " pdb=" C ASP C 388 " pdb=" CB ASP C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2081 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C39 6OU C 502 " -0.074 2.00e-02 2.50e+03 7.38e-02 5.45e+01 pdb=" C40 6OU C 502 " 0.074 2.00e-02 2.50e+03 pdb=" C41 6OU C 502 " 0.074 2.00e-02 2.50e+03 pdb=" C42 6OU C 502 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 6OU D 504 " -0.074 2.00e-02 2.50e+03 7.36e-02 5.41e+01 pdb=" C40 6OU D 504 " 0.074 2.00e-02 2.50e+03 pdb=" C41 6OU D 504 " 0.074 2.00e-02 2.50e+03 pdb=" C42 6OU D 504 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 6OU A 502 " 0.074 2.00e-02 2.50e+03 7.36e-02 5.41e+01 pdb=" C40 6OU A 502 " -0.074 2.00e-02 2.50e+03 pdb=" C41 6OU A 502 " -0.074 2.00e-02 2.50e+03 pdb=" C42 6OU A 502 " 0.074 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 5052 2.92 - 3.41: 13397 3.41 - 3.91: 22491 3.91 - 4.40: 25598 4.40 - 4.90: 41712 Nonbonded interactions: 108250 Sorted by model distance: nonbonded pdb=" N LEU C 39 " pdb=" N PHE C 40 " model vdw 2.419 2.560 nonbonded pdb=" N LEU B 39 " pdb=" N PHE B 40 " model vdw 2.419 2.560 nonbonded pdb=" N LEU A 39 " pdb=" N PHE A 40 " model vdw 2.419 2.560 nonbonded pdb=" N LEU D 39 " pdb=" N PHE D 40 " model vdw 2.420 2.560 nonbonded pdb=" OG SER D 51 " pdb=" NH2 ARG D 111 " model vdw 2.537 3.120 ... (remaining 108245 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' and (resid 10 through 415 or (resid 502 and (name C19 or name C20 or \ name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ C45 or name O30 or name O32)) or (resid 503 and (name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C21 or na \ me C27 or name C28 or name C31 or name C33 or name C34 or name C35 or name C36 o \ r name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C \ 43 or name N29 or name O17 or name O18 or name O22 or name O24 or name O25 or na \ me O26 or name O30 or name O32 or name P23)) or (resid 505 and (name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name O22 or name O30 or name O32)))) selection = (chain 'B' and (resid 10 through 415 or (resid 502 and (name C19 or name C20 or \ name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ C45 or name O30 or name O32)) or (resid 503 and (name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C21 or na \ me C27 or name C28 or name C31 or name C33 or name C34 or name C35 or name C36 o \ r name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C \ 43 or name N29 or name O17 or name O18 or name O22 or name O24 or name O25 or na \ me O26 or name O30 or name O32 or name P23)) or (resid 505 and (name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name O22 or name O30 or name O32)))) selection = (chain 'C' and (resid 10 through 415 or (resid 502 and (name C19 or name C20 or \ name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ C45 or name O30 or name O32)) or (resid 503 and (name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C21 or na \ me C27 or name C28 or name C31 or name C33 or name C34 or name C35 or name C36 o \ r name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C \ 43 or name N29 or name O17 or name O18 or name O22 or name O24 or name O25 or na \ me O26 or name O30 or name O32 or name P23)) or (resid 505 and (name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name O22 or name O30 or name O32)))) selection = (chain 'D' and (resid 10 through 415 or (resid 502 and (name C19 or name C20 or \ name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ C45 or name O30 or name O32)) or (resid 503 and (name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C16 or name C19 or name C20 or name C21 or na \ me C27 or name C28 or name C31 or name C33 or name C34 or name C35 or name C36 o \ r name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C \ 43 or name N29 or name O17 or name O18 or name O22 or name O24 or name O25 or na \ me O26 or name O30 or name O32 or name P23)) or (resid 505 and (name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name O22 or name O30 or name O32)))) } 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.840 Find NCS groups from input model: 0.420 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:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 13304 Z= 0.429 Angle : 1.187 8.630 17978 Z= 0.654 Chirality : 0.065 0.233 2084 Planarity : 0.015 0.128 2200 Dihedral : 18.789 165.679 5188 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.21), residues: 1552 helix: -0.97 (0.14), residues: 1028 sheet: -0.53 (0.57), residues: 68 loop : 0.74 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 169 TYR 0.018 0.003 TYR C 186 PHE 0.020 0.003 PHE B 365 TRP 0.041 0.004 TRP D 264 HIS 0.014 0.006 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00871 (13304) covalent geometry : angle 1.18746 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.14066 ( 824) hydrogen bonds : angle 6.53098 ( 2364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9513 (mt) cc_final: 0.9255 (mt) REVERT: A 234 GLU cc_start: 0.8875 (pt0) cc_final: 0.8524 (tp30) REVERT: A 289 MET cc_start: 0.9145 (mmm) cc_final: 0.8944 (mmm) REVERT: A 298 LYS cc_start: 0.9447 (ptpt) cc_final: 0.9068 (ptpp) REVERT: B 85 LEU cc_start: 0.9510 (mt) cc_final: 0.9254 (mt) REVERT: B 234 GLU cc_start: 0.8867 (pt0) cc_final: 0.8510 (tp30) REVERT: B 298 LYS cc_start: 0.9435 (ptpt) cc_final: 0.9077 (ptpp) REVERT: C 85 LEU cc_start: 0.9512 (mt) cc_final: 0.9262 (mt) REVERT: C 234 GLU cc_start: 0.8877 (pt0) cc_final: 0.8523 (tp30) REVERT: C 289 MET cc_start: 0.9147 (mmm) cc_final: 0.8846 (mmm) REVERT: C 298 LYS cc_start: 0.9429 (ptpt) cc_final: 0.9076 (ptpp) REVERT: D 85 LEU cc_start: 0.9510 (mt) cc_final: 0.9261 (mt) REVERT: D 234 GLU cc_start: 0.8869 (pt0) cc_final: 0.8535 (tp30) REVERT: D 298 LYS cc_start: 0.9435 (ptpt) cc_final: 0.9060 (ptpp) outliers start: 0 outliers final: 1 residues processed: 197 average time/residue: 0.7295 time to fit residues: 153.8741 Evaluate side-chains 102 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 253 GLN B 119 GLN B 253 GLN C 119 GLN C 253 GLN D 119 GLN D 253 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.098033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.066218 restraints weight = 28635.295| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.87 r_work: 0.2875 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13304 Z= 0.178 Angle : 0.725 9.792 17978 Z= 0.342 Chirality : 0.046 0.229 2084 Planarity : 0.005 0.031 2200 Dihedral : 18.606 166.491 2230 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.08 % Allowed : 8.56 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1552 helix: 0.50 (0.16), residues: 1020 sheet: -0.19 (0.57), residues: 88 loop : 1.36 (0.35), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 124 TYR 0.013 0.002 TYR A 170 PHE 0.009 0.001 PHE B 40 TRP 0.012 0.002 TRP A 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00425 (13304) covalent geometry : angle 0.72507 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04242 ( 824) hydrogen bonds : angle 4.50898 ( 2364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9088 (pp) REVERT: A 164 ASN cc_start: 0.8989 (m110) cc_final: 0.8598 (m110) REVERT: A 234 GLU cc_start: 0.8816 (pt0) cc_final: 0.8546 (pp20) REVERT: A 369 MET cc_start: 0.8979 (tpp) cc_final: 0.8773 (tpp) REVERT: B 55 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9090 (pp) REVERT: B 164 ASN cc_start: 0.8986 (m110) cc_final: 0.8593 (m110) REVERT: B 234 GLU cc_start: 0.8827 (pt0) cc_final: 0.8369 (pp20) REVERT: C 55 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9088 (pp) REVERT: C 164 ASN cc_start: 0.8986 (m110) cc_final: 0.8602 (m110) REVERT: C 234 GLU cc_start: 0.8816 (pt0) cc_final: 0.8357 (pp20) REVERT: C 314 ILE cc_start: 0.8927 (pt) cc_final: 0.8726 (pp) REVERT: D 55 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9085 (pp) REVERT: D 164 ASN cc_start: 0.8981 (m110) cc_final: 0.8596 (m110) REVERT: D 234 GLU cc_start: 0.8821 (pt0) cc_final: 0.8547 (pp20) REVERT: D 369 MET cc_start: 0.8990 (tpp) cc_final: 0.8747 (tpp) outliers start: 28 outliers final: 4 residues processed: 147 average time/residue: 0.6236 time to fit residues: 99.4787 Evaluate side-chains 106 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 82 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 117 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066686 restraints weight = 28792.323| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.90 r_work: 0.2898 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13304 Z= 0.139 Angle : 0.660 10.521 17978 Z= 0.304 Chirality : 0.043 0.183 2084 Planarity : 0.004 0.033 2200 Dihedral : 17.241 174.974 2228 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.71 % Allowed : 12.13 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.22), residues: 1552 helix: 0.84 (0.16), residues: 1040 sheet: 0.44 (0.62), residues: 88 loop : 1.60 (0.34), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 268 TYR 0.013 0.001 TYR A 170 PHE 0.009 0.001 PHE B 40 TRP 0.008 0.001 TRP B 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00325 (13304) covalent geometry : angle 0.66044 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03762 ( 824) hydrogen bonds : angle 4.24035 ( 2364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9049 (pt) REVERT: A 164 ASN cc_start: 0.9017 (m110) cc_final: 0.8621 (m110) REVERT: A 234 GLU cc_start: 0.8847 (pt0) cc_final: 0.8498 (pp20) REVERT: A 369 MET cc_start: 0.8865 (tpp) cc_final: 0.8534 (tpp) REVERT: A 394 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8767 (tppp) REVERT: B 55 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9044 (pt) REVERT: B 107 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8641 (pp) REVERT: B 164 ASN cc_start: 0.8998 (m110) cc_final: 0.8595 (m110) REVERT: B 234 GLU cc_start: 0.8844 (pt0) cc_final: 0.8504 (pp20) REVERT: B 334 MET cc_start: 0.8890 (mmm) cc_final: 0.8475 (tpt) REVERT: B 369 MET cc_start: 0.8962 (tpp) cc_final: 0.8616 (tpp) REVERT: C 55 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9038 (pt) REVERT: C 107 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8610 (pp) REVERT: C 164 ASN cc_start: 0.8995 (m110) cc_final: 0.8601 (m110) REVERT: C 234 GLU cc_start: 0.8856 (pt0) cc_final: 0.8520 (pp20) REVERT: C 289 MET cc_start: 0.9132 (mmm) cc_final: 0.8891 (mmm) REVERT: C 334 MET cc_start: 0.8887 (mmm) cc_final: 0.8457 (tpt) REVERT: C 369 MET cc_start: 0.8914 (tpp) cc_final: 0.8582 (tpp) REVERT: C 394 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8779 (tppp) REVERT: D 55 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9039 (pt) REVERT: D 107 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8600 (pp) REVERT: D 164 ASN cc_start: 0.8983 (m110) cc_final: 0.8592 (m110) REVERT: D 234 GLU cc_start: 0.8852 (pt0) cc_final: 0.8501 (pp20) REVERT: D 369 MET cc_start: 0.8916 (tpp) cc_final: 0.8664 (tpp) outliers start: 23 outliers final: 5 residues processed: 134 average time/residue: 0.6314 time to fit residues: 91.8381 Evaluate side-chains 115 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 7 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 0.0670 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.098692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067118 restraints weight = 28833.173| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.90 r_work: 0.2905 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13304 Z= 0.124 Angle : 0.644 11.037 17978 Z= 0.297 Chirality : 0.042 0.171 2084 Planarity : 0.004 0.031 2200 Dihedral : 16.662 179.452 2228 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.08 % Allowed : 12.43 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1552 helix: 1.13 (0.17), residues: 1052 sheet: 0.34 (0.62), residues: 88 loop : 1.15 (0.35), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 268 TYR 0.012 0.001 TYR C 170 PHE 0.007 0.001 PHE D 40 TRP 0.006 0.001 TRP D 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00290 (13304) covalent geometry : angle 0.64402 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03530 ( 824) hydrogen bonds : angle 4.16382 ( 2364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9047 (pt) REVERT: A 107 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8677 (pp) REVERT: A 164 ASN cc_start: 0.9001 (m110) cc_final: 0.8617 (m110) REVERT: A 234 GLU cc_start: 0.8847 (pt0) cc_final: 0.8558 (pp20) REVERT: A 394 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8769 (tppp) REVERT: B 55 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9034 (pt) REVERT: B 107 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8684 (pp) REVERT: B 164 ASN cc_start: 0.9003 (m110) cc_final: 0.8586 (m110) REVERT: B 234 GLU cc_start: 0.8849 (pt0) cc_final: 0.8564 (pp20) REVERT: C 55 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9028 (pt) REVERT: C 107 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8635 (pp) REVERT: C 164 ASN cc_start: 0.8985 (m110) cc_final: 0.8591 (m110) REVERT: C 234 GLU cc_start: 0.8852 (pt0) cc_final: 0.8563 (pp20) REVERT: C 289 MET cc_start: 0.9187 (mmm) cc_final: 0.8911 (mmm) REVERT: C 334 MET cc_start: 0.8939 (mmm) cc_final: 0.8555 (tpt) REVERT: C 394 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8770 (tppp) REVERT: D 55 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9025 (pt) REVERT: D 107 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8634 (pp) REVERT: D 164 ASN cc_start: 0.8996 (m110) cc_final: 0.8601 (m110) REVERT: D 234 GLU cc_start: 0.8849 (pt0) cc_final: 0.8560 (pp20) REVERT: D 369 MET cc_start: 0.8898 (tpp) cc_final: 0.8656 (tpp) outliers start: 28 outliers final: 9 residues processed: 130 average time/residue: 0.5700 time to fit residues: 80.6286 Evaluate side-chains 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 107 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 0.0270 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.099172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.067690 restraints weight = 28951.264| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.91 r_work: 0.2928 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13304 Z= 0.121 Angle : 0.644 11.194 17978 Z= 0.294 Chirality : 0.042 0.203 2084 Planarity : 0.004 0.028 2200 Dihedral : 15.960 176.213 2228 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.05 % Allowed : 12.43 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.23), residues: 1552 helix: 1.32 (0.17), residues: 1052 sheet: 0.24 (0.60), residues: 88 loop : 1.05 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 268 TYR 0.010 0.001 TYR D 128 PHE 0.005 0.001 PHE D 40 TRP 0.006 0.001 TRP B 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00281 (13304) covalent geometry : angle 0.64370 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03378 ( 824) hydrogen bonds : angle 4.08492 ( 2364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8991 (pt) REVERT: A 164 ASN cc_start: 0.8987 (m110) cc_final: 0.8599 (m110) REVERT: A 234 GLU cc_start: 0.8844 (pt0) cc_final: 0.8541 (pp20) REVERT: A 394 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8732 (tppp) REVERT: B 55 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8935 (pp) REVERT: B 164 ASN cc_start: 0.8981 (m110) cc_final: 0.8583 (m110) REVERT: B 229 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8160 (tmtt) REVERT: B 234 GLU cc_start: 0.8842 (pt0) cc_final: 0.8543 (pp20) REVERT: B 334 MET cc_start: 0.8794 (tpt) cc_final: 0.8396 (tpt) REVERT: B 369 MET cc_start: 0.8870 (tpp) cc_final: 0.8635 (tpp) REVERT: C 55 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8984 (pt) REVERT: C 164 ASN cc_start: 0.8988 (m110) cc_final: 0.8599 (m110) REVERT: C 234 GLU cc_start: 0.8838 (pt0) cc_final: 0.8540 (pp20) REVERT: C 289 MET cc_start: 0.9162 (mmm) cc_final: 0.8908 (mmm) REVERT: C 334 MET cc_start: 0.8897 (mmm) cc_final: 0.8487 (tpt) REVERT: C 394 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8727 (tppp) REVERT: D 55 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8982 (pt) REVERT: D 164 ASN cc_start: 0.8983 (m110) cc_final: 0.8594 (m110) REVERT: D 234 GLU cc_start: 0.8830 (pt0) cc_final: 0.8534 (pp20) REVERT: D 369 MET cc_start: 0.8860 (tpp) cc_final: 0.8499 (tpp) outliers start: 41 outliers final: 12 residues processed: 141 average time/residue: 0.5670 time to fit residues: 87.2544 Evaluate side-chains 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 82 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.098802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.067174 restraints weight = 28571.530| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.90 r_work: 0.2916 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13304 Z= 0.129 Angle : 0.668 11.588 17978 Z= 0.304 Chirality : 0.043 0.220 2084 Planarity : 0.004 0.029 2200 Dihedral : 15.708 172.966 2228 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.64 % Allowed : 15.48 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.23), residues: 1552 helix: 1.40 (0.17), residues: 1048 sheet: 0.18 (0.60), residues: 88 loop : 1.05 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 268 TYR 0.008 0.001 TYR B 170 PHE 0.004 0.001 PHE A 366 TRP 0.007 0.001 TRP B 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00308 (13304) covalent geometry : angle 0.66815 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03426 ( 824) hydrogen bonds : angle 4.12236 ( 2364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8973 (pt) REVERT: A 164 ASN cc_start: 0.9004 (m110) cc_final: 0.8600 (m110) REVERT: A 234 GLU cc_start: 0.8834 (pt0) cc_final: 0.8537 (pp20) REVERT: A 369 MET cc_start: 0.8824 (tpp) cc_final: 0.8574 (tpp) REVERT: A 394 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8726 (tppp) REVERT: B 55 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8965 (pt) REVERT: B 164 ASN cc_start: 0.8971 (m110) cc_final: 0.8551 (m110) REVERT: B 229 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8168 (tmtt) REVERT: B 234 GLU cc_start: 0.8837 (pt0) cc_final: 0.8546 (pp20) REVERT: C 55 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8971 (pt) REVERT: C 164 ASN cc_start: 0.8966 (m110) cc_final: 0.8557 (m110) REVERT: C 234 GLU cc_start: 0.8832 (pt0) cc_final: 0.8538 (pp20) REVERT: C 289 MET cc_start: 0.9162 (mmm) cc_final: 0.8890 (mmm) REVERT: C 334 MET cc_start: 0.8939 (mmm) cc_final: 0.8552 (tpt) REVERT: C 394 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8731 (tppp) REVERT: D 55 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8963 (pt) REVERT: D 164 ASN cc_start: 0.8974 (m110) cc_final: 0.8568 (m110) REVERT: D 229 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8181 (tmtt) REVERT: D 234 GLU cc_start: 0.8831 (pt0) cc_final: 0.8539 (pp20) outliers start: 22 outliers final: 11 residues processed: 118 average time/residue: 0.7035 time to fit residues: 90.1265 Evaluate side-chains 116 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 229 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 127 optimal weight: 0.0470 chunk 121 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 GLN C 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.098656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.066949 restraints weight = 28619.425| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.89 r_work: 0.2914 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13304 Z= 0.139 Angle : 0.692 14.543 17978 Z= 0.313 Chirality : 0.043 0.230 2084 Planarity : 0.004 0.028 2200 Dihedral : 15.450 170.423 2228 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.08 % Allowed : 15.55 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.23), residues: 1552 helix: 1.37 (0.17), residues: 1048 sheet: 0.14 (0.59), residues: 88 loop : 1.04 (0.34), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 268 TYR 0.009 0.001 TYR C 128 PHE 0.004 0.001 PHE A 366 TRP 0.008 0.001 TRP A 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00334 (13304) covalent geometry : angle 0.69247 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03459 ( 824) hydrogen bonds : angle 4.15786 ( 2364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8931 (pp) REVERT: A 164 ASN cc_start: 0.8994 (m110) cc_final: 0.8565 (m110) REVERT: A 234 GLU cc_start: 0.8837 (pt0) cc_final: 0.8551 (pp20) REVERT: A 334 MET cc_start: 0.8604 (tpt) cc_final: 0.8300 (tpp) REVERT: A 394 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8717 (tppp) REVERT: B 55 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8933 (pp) REVERT: B 104 LEU cc_start: 0.9359 (tp) cc_final: 0.9051 (pt) REVERT: B 164 ASN cc_start: 0.8991 (m110) cc_final: 0.8559 (m110) REVERT: B 229 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8174 (tmtt) REVERT: B 234 GLU cc_start: 0.8829 (pt0) cc_final: 0.8553 (pp20) REVERT: C 55 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8910 (pp) REVERT: C 164 ASN cc_start: 0.8988 (m110) cc_final: 0.8560 (m110) REVERT: C 234 GLU cc_start: 0.8829 (pt0) cc_final: 0.8547 (pp20) REVERT: C 289 MET cc_start: 0.9175 (mmm) cc_final: 0.8900 (mmm) REVERT: C 334 MET cc_start: 0.8930 (mmm) cc_final: 0.8554 (tpt) REVERT: C 394 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8734 (tppp) REVERT: D 55 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8908 (pp) REVERT: D 164 ASN cc_start: 0.8993 (m110) cc_final: 0.8567 (m110) REVERT: D 229 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8193 (tmtt) REVERT: D 234 GLU cc_start: 0.8826 (pt0) cc_final: 0.8550 (pp20) REVERT: D 334 MET cc_start: 0.8653 (tpt) cc_final: 0.8349 (tpp) REVERT: D 369 MET cc_start: 0.8850 (tpp) cc_final: 0.8621 (tpp) outliers start: 28 outliers final: 10 residues processed: 118 average time/residue: 0.6933 time to fit residues: 88.8386 Evaluate side-chains 111 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 229 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN D 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.097431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065362 restraints weight = 28717.761| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.89 r_work: 0.2854 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13304 Z= 0.180 Angle : 0.703 11.114 17978 Z= 0.322 Chirality : 0.046 0.284 2084 Planarity : 0.004 0.027 2200 Dihedral : 15.307 168.872 2228 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.08 % Allowed : 15.70 % Favored : 82.22 % 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: 1.61 (0.23), residues: 1552 helix: 1.35 (0.17), residues: 1044 sheet: -0.08 (0.60), residues: 88 loop : 0.91 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.009 0.001 TYR A 170 PHE 0.005 0.001 PHE A 302 TRP 0.009 0.001 TRP C 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00431 (13304) covalent geometry : angle 0.70353 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03602 ( 824) hydrogen bonds : angle 4.21507 ( 2364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8968 (t0) cc_final: 0.8486 (t0) REVERT: A 55 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 82 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8239 (pt) REVERT: A 234 GLU cc_start: 0.8872 (pt0) cc_final: 0.8592 (pp20) REVERT: A 394 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8739 (tppp) REVERT: B 55 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8983 (pp) REVERT: B 82 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8242 (pt) REVERT: B 104 LEU cc_start: 0.9312 (tp) cc_final: 0.8957 (pt) REVERT: B 234 GLU cc_start: 0.8861 (pt0) cc_final: 0.8573 (pp20) REVERT: B 334 MET cc_start: 0.8605 (tpt) cc_final: 0.8281 (tpp) REVERT: C 55 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8971 (pp) REVERT: C 82 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8197 (pt) REVERT: C 234 GLU cc_start: 0.8861 (pt0) cc_final: 0.8581 (pp20) REVERT: C 289 MET cc_start: 0.9199 (mmm) cc_final: 0.8937 (mmm) REVERT: C 334 MET cc_start: 0.9008 (mmm) cc_final: 0.8679 (tpt) REVERT: C 394 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8738 (tppp) REVERT: D 55 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8963 (pp) REVERT: D 82 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8216 (pt) REVERT: D 234 GLU cc_start: 0.8855 (pt0) cc_final: 0.8579 (pp20) outliers start: 28 outliers final: 8 residues processed: 119 average time/residue: 0.5895 time to fit residues: 76.5965 Evaluate side-chains 108 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 82 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 133 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.098668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.066848 restraints weight = 28602.544| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.92 r_work: 0.2902 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13304 Z= 0.135 Angle : 0.727 11.579 17978 Z= 0.323 Chirality : 0.044 0.229 2084 Planarity : 0.004 0.027 2200 Dihedral : 14.996 167.481 2228 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.64 % Allowed : 16.07 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.23), residues: 1552 helix: 1.41 (0.17), residues: 1052 sheet: -0.05 (0.59), residues: 88 loop : 0.86 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 374 TYR 0.010 0.001 TYR C 128 PHE 0.003 0.001 PHE A 366 TRP 0.009 0.001 TRP C 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00324 (13304) covalent geometry : angle 0.72697 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03406 ( 824) hydrogen bonds : angle 4.21239 ( 2364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8964 (pt) REVERT: A 82 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8178 (pt) REVERT: A 234 GLU cc_start: 0.8831 (pt0) cc_final: 0.8547 (pp20) REVERT: A 334 MET cc_start: 0.8575 (tpt) cc_final: 0.8305 (tpp) REVERT: A 394 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8726 (tptt) REVERT: B 55 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8979 (pt) REVERT: B 82 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8141 (pt) REVERT: B 104 LEU cc_start: 0.9195 (tp) cc_final: 0.8799 (pt) REVERT: B 229 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8181 (tmtt) REVERT: B 234 GLU cc_start: 0.8830 (pt0) cc_final: 0.8547 (pp20) REVERT: B 334 MET cc_start: 0.8653 (tpt) cc_final: 0.8347 (tpp) REVERT: C 55 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8968 (pt) REVERT: C 82 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8215 (pt) REVERT: C 234 GLU cc_start: 0.8829 (pt0) cc_final: 0.8546 (pp20) REVERT: C 289 MET cc_start: 0.9164 (mmm) cc_final: 0.8902 (mmm) REVERT: C 334 MET cc_start: 0.8959 (mmm) cc_final: 0.8585 (tpt) REVERT: C 394 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8683 (tptt) REVERT: D 55 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8969 (pt) REVERT: D 82 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8222 (pt) REVERT: D 229 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8184 (tmtt) REVERT: D 234 GLU cc_start: 0.8822 (pt0) cc_final: 0.8546 (pp20) REVERT: D 334 MET cc_start: 0.8599 (tpt) cc_final: 0.8339 (tpp) outliers start: 22 outliers final: 10 residues processed: 114 average time/residue: 0.6329 time to fit residues: 78.6444 Evaluate side-chains 114 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 229 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.098879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.066854 restraints weight = 28674.419| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.92 r_work: 0.2908 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13304 Z= 0.135 Angle : 0.757 15.329 17978 Z= 0.332 Chirality : 0.043 0.224 2084 Planarity : 0.004 0.027 2200 Dihedral : 14.729 164.768 2228 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.49 % Allowed : 16.44 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.23), residues: 1552 helix: 1.42 (0.17), residues: 1052 sheet: -0.13 (0.57), residues: 88 loop : 0.83 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 374 TYR 0.007 0.001 TYR C 175 PHE 0.003 0.001 PHE A 366 TRP 0.009 0.001 TRP A 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00326 (13304) covalent geometry : angle 0.75702 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03402 ( 824) hydrogen bonds : angle 4.24458 ( 2364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9362 (mm) REVERT: A 55 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8923 (pp) REVERT: A 82 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8198 (pt) REVERT: A 104 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8594 (pt) REVERT: A 234 GLU cc_start: 0.8824 (pt0) cc_final: 0.8547 (pp20) REVERT: A 334 MET cc_start: 0.8605 (tpt) cc_final: 0.8342 (tpp) REVERT: A 394 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8683 (tptt) REVERT: B 55 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8944 (pp) REVERT: B 82 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8148 (pt) REVERT: B 104 LEU cc_start: 0.9178 (tp) cc_final: 0.8752 (pt) REVERT: B 234 GLU cc_start: 0.8829 (pt0) cc_final: 0.8555 (pp20) REVERT: B 334 MET cc_start: 0.8670 (tpt) cc_final: 0.8355 (tpp) REVERT: C 55 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8928 (pp) REVERT: C 82 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8226 (pt) REVERT: C 104 LEU cc_start: 0.9057 (tp) cc_final: 0.8583 (pt) REVERT: C 234 GLU cc_start: 0.8829 (pt0) cc_final: 0.8552 (pp20) REVERT: C 289 MET cc_start: 0.9157 (mmm) cc_final: 0.8899 (mmm) REVERT: C 334 MET cc_start: 0.8958 (mmm) cc_final: 0.8573 (tpt) REVERT: C 394 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8684 (tptt) REVERT: D 55 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8909 (pp) REVERT: D 82 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8227 (pt) REVERT: D 229 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8193 (tmtt) REVERT: D 234 GLU cc_start: 0.8814 (pt0) cc_final: 0.8545 (pp20) REVERT: D 334 MET cc_start: 0.8606 (tpt) cc_final: 0.8350 (tpp) outliers start: 20 outliers final: 10 residues processed: 112 average time/residue: 0.6386 time to fit residues: 77.7163 Evaluate side-chains 116 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 229 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.098708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.066870 restraints weight = 28627.476| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.92 r_work: 0.2908 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13304 Z= 0.140 Angle : 0.734 11.752 17978 Z= 0.330 Chirality : 0.045 0.302 2084 Planarity : 0.004 0.027 2200 Dihedral : 14.579 162.666 2228 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.64 % Allowed : 16.59 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.23), residues: 1552 helix: 1.42 (0.17), residues: 1052 sheet: -0.21 (0.56), residues: 88 loop : 0.84 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 374 TYR 0.010 0.001 TYR A 26 PHE 0.003 0.001 PHE B 366 TRP 0.009 0.001 TRP A 264 HIS 0.003 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00337 (13304) covalent geometry : angle 0.73372 (17976) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03366 ( 824) hydrogen bonds : angle 4.24564 ( 2364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4160.28 seconds wall clock time: 71 minutes 45.78 seconds (4305.78 seconds total)