Starting phenix.real_space_refine on Fri Oct 10 16:04:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chm_45590/10_2025/9chm_45590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chm_45590/10_2025/9chm_45590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9chm_45590/10_2025/9chm_45590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chm_45590/10_2025/9chm_45590.map" model { file = "/net/cci-nas-00/data/ceres_data/9chm_45590/10_2025/9chm_45590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chm_45590/10_2025/9chm_45590.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4729 2.51 5 N 1230 2.21 5 O 1487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7498 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1474 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 6, 'TRANS': 177} Chain: "B" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "D" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2008 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Time building chain proxies: 1.73, per 1000 atoms: 0.23 Number of scatterers: 7498 At special positions: 0 Unit cell: (101.87, 106.045, 120.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1487 8.00 N 1230 7.00 C 4729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 162 " distance=2.04 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: 0.57 Conformation dependent library (CDL) restraints added in 386.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 30.7% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'E' and resid 372 through 387 removed outlier: 3.546A pdb=" N PHE E 379 " --> pdb=" O TYR E 375 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU E 380 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL E 381 " --> pdb=" O ARG E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 395 Processing helix chain 'E' and resid 397 through 410 Processing helix chain 'E' and resid 414 through 423 removed outlier: 4.300A pdb=" N TYR E 418 " --> pdb=" O GLY E 414 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.532A pdb=" N LYS E 433 " --> pdb=" O LYS E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 454 Processing helix chain 'E' and resid 464 through 472 Processing helix chain 'E' and resid 473 through 483 Processing helix chain 'E' and resid 492 through 503 removed outlier: 3.590A pdb=" N LEU E 503 " --> pdb=" O ALA E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 513 removed outlier: 4.353A pdb=" N GLY E 513 " --> pdb=" O CYS E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 532 Processing helix chain 'E' and resid 538 through 554 removed outlier: 3.625A pdb=" N ARG E 542 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.261A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 19 " --> pdb=" O VAL B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.688A pdb=" N SER B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 153 removed outlier: 3.505A pdb=" N ARG B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'B' and resid 255 through 261 removed outlier: 4.016A pdb=" N GLU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 removed outlier: 4.032A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.795A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 removed outlier: 3.646A pdb=" N PHE C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 Proline residue: C 220 - end of helix No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'D' and resid 8 through 21 removed outlier: 3.955A pdb=" N LEU D 12 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 141 through 152 Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.594A pdb=" N PHE D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Proline residue: D 220 - end of helix No H-bonds generated for 'chain 'D' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'E' and resid 456 through 457 Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 62 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 71 removed outlier: 7.527A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 48 " --> pdb=" O SER B 39 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER B 230 " --> pdb=" O PRO B 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 104 removed outlier: 3.684A pdb=" N ASN C 177 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL C 167 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 163 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AA6, first strand: chain 'B' and resid 157 through 158 removed outlier: 3.649A pdb=" N VAL B 158 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 207 " --> pdb=" O VAL B 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 166 through 172 removed outlier: 3.988A pdb=" N ASN B 177 " --> pdb=" O GLU D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 62 Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 62 removed outlier: 3.508A pdb=" N MET C 116 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 182 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL D 167 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 166 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER D 161 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 170 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER D 172 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA D 157 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 71 removed outlier: 3.960A pdb=" N MET C 68 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 70 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA C 26 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 48 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 59 through 62 Processing sheet with id=AB3, first strand: chain 'D' and resid 69 through 71 removed outlier: 3.577A pdb=" N ALA D 26 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLU D 25 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N MET D 40 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N CYS D 27 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS D 240 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR D 224 " --> pdb=" O LYS D 240 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 942 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: 0.98 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2461 1.34 - 1.46: 1108 1.46 - 1.58: 3949 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 7602 Sorted by residual: bond pdb=" CA TYR E 418 " pdb=" C TYR E 418 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.35e-02 5.49e+03 2.47e+00 bond pdb=" C ALA E 474 " pdb=" N PRO E 475 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 1.99e+00 bond pdb=" CA THR C 216 " pdb=" C THR C 216 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.80e-02 3.09e+03 1.85e+00 bond pdb=" CB GLN D 125 " pdb=" CG GLN D 125 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CA GLY E 520 " pdb=" C GLY E 520 " ideal model delta sigma weight residual 1.516 1.502 0.014 1.12e-02 7.97e+03 1.56e+00 ... (remaining 7597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 9998 2.18 - 4.37: 213 4.37 - 6.55: 37 6.55 - 8.74: 14 8.74 - 10.92: 3 Bond angle restraints: 10265 Sorted by residual: angle pdb=" N VAL E 386 " pdb=" CA VAL E 386 " pdb=" C VAL E 386 " ideal model delta sigma weight residual 113.00 107.62 5.38 1.30e+00 5.92e-01 1.72e+01 angle pdb=" CA GLN C 125 " pdb=" CB GLN C 125 " pdb=" CG GLN C 125 " ideal model delta sigma weight residual 114.10 121.87 -7.77 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CA TYR E 408 " pdb=" CB TYR E 408 " pdb=" CG TYR E 408 " ideal model delta sigma weight residual 113.90 120.81 -6.91 1.80e+00 3.09e-01 1.47e+01 angle pdb=" C LEU E 417 " pdb=" N TYR E 418 " pdb=" CA TYR E 418 " ideal model delta sigma weight residual 120.31 114.93 5.38 1.52e+00 4.33e-01 1.25e+01 angle pdb=" N GLY B 166 " pdb=" CA GLY B 166 " pdb=" C GLY B 166 " ideal model delta sigma weight residual 110.38 114.89 -4.51 1.28e+00 6.10e-01 1.24e+01 ... (remaining 10260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4062 17.89 - 35.78: 502 35.78 - 53.66: 102 53.66 - 71.55: 19 71.55 - 89.44: 12 Dihedral angle restraints: 4697 sinusoidal: 1876 harmonic: 2821 Sorted by residual: dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 162 " pdb=" CB CYS D 162 " ideal model delta sinusoidal sigma weight residual -86.00 -1.49 -84.51 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CA MET B 40 " pdb=" C MET B 40 " pdb=" N ASP B 41 " pdb=" CA ASP B 41 " ideal model delta harmonic sigma weight residual -180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LYS E 505 " pdb=" C LYS E 505 " pdb=" N GLN E 506 " pdb=" CA GLN E 506 " ideal model delta harmonic sigma weight residual -180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 4694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 858 0.041 - 0.082: 245 0.082 - 0.123: 90 0.123 - 0.164: 12 0.164 - 0.205: 2 Chirality restraints: 1207 Sorted by residual: chirality pdb=" CB THR E 385 " pdb=" CA THR E 385 " pdb=" OG1 THR E 385 " pdb=" CG2 THR E 385 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU B 52 " pdb=" CB LEU B 52 " pdb=" CD1 LEU B 52 " pdb=" CD2 LEU B 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CA PHE E 545 " pdb=" N PHE E 545 " pdb=" C PHE E 545 " pdb=" CB PHE E 545 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 1204 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 408 " -0.023 2.00e-02 2.50e+03 1.71e-02 5.83e+00 pdb=" CG TYR E 408 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 408 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR E 408 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 408 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 408 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 408 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 408 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 541 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C PRO E 541 " -0.030 2.00e-02 2.50e+03 pdb=" O PRO E 541 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG E 542 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 2 " -0.009 2.00e-02 2.50e+03 1.24e-02 2.70e+00 pdb=" CG PHE B 2 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 2 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 2 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 2 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 2 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 2 " -0.000 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 428 2.72 - 3.27: 7965 3.27 - 3.81: 12047 3.81 - 4.36: 14012 4.36 - 4.90: 23175 Nonbonded interactions: 57627 Sorted by model distance: nonbonded pdb=" OG SER D 43 " pdb=" OH TYR D 211 " model vdw 2.176 3.040 nonbonded pdb=" O ARG B 149 " pdb=" OG SER B 152 " model vdw 2.203 3.040 nonbonded pdb=" O SER C 31 " pdb=" OH TYR C 60 " model vdw 2.221 3.040 nonbonded pdb=" N GLU B 55 " pdb=" OE1 GLU B 55 " model vdw 2.222 3.120 nonbonded pdb=" O ALA E 412 " pdb=" NZ LYS E 416 " model vdw 2.223 3.120 ... (remaining 57622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.004 0.038 7605 Z= 0.192 Angle : 0.822 10.922 10271 Z= 0.441 Chirality : 0.044 0.205 1207 Planarity : 0.004 0.039 1316 Dihedral : 16.491 89.439 2856 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.35 % Allowed : 28.34 % Favored : 71.31 % 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 aren not related in a simple way. whole: -0.84 (0.28), residues: 959 helix: 1.05 (0.35), residues: 227 sheet: -0.83 (0.29), residues: 344 loop : -1.14 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 149 TYR 0.041 0.002 TYR E 408 PHE 0.028 0.002 PHE B 2 TRP 0.008 0.001 TRP E 428 HIS 0.007 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7602) covalent geometry : angle 0.81982 (10265) SS BOND : bond 0.00582 ( 3) SS BOND : angle 2.56568 ( 6) hydrogen bonds : bond 0.27452 ( 336) hydrogen bonds : angle 9.11428 ( 942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8857 (ppp) cc_final: 0.8343 (ppp) REVERT: B 44 HIS cc_start: 0.8964 (m90) cc_final: 0.8670 (m90) outliers start: 3 outliers final: 2 residues processed: 120 average time/residue: 0.0988 time to fit residues: 15.5370 Evaluate side-chains 112 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 490 ASN Chi-restraints excluded: chain E residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.071971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.050586 restraints weight = 33041.752| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 6.77 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7605 Z= 0.197 Angle : 0.694 8.323 10271 Z= 0.361 Chirality : 0.045 0.149 1207 Planarity : 0.004 0.051 1316 Dihedral : 4.670 20.632 1024 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.78 % Allowed : 24.79 % Favored : 71.43 % 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 aren not related in a simple way. whole: -0.83 (0.27), residues: 959 helix: 0.85 (0.33), residues: 255 sheet: -0.45 (0.28), residues: 337 loop : -1.57 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 61 TYR 0.037 0.003 TYR E 408 PHE 0.016 0.002 PHE E 545 TRP 0.013 0.002 TRP C 28 HIS 0.004 0.001 HIS E 372 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7602) covalent geometry : angle 0.68938 (10265) SS BOND : bond 0.01054 ( 3) SS BOND : angle 3.33033 ( 6) hydrogen bonds : bond 0.04718 ( 336) hydrogen bonds : angle 6.32127 ( 942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 431 MET cc_start: 0.9487 (ptp) cc_final: 0.9187 (ppp) REVERT: B 135 CYS cc_start: 0.7898 (t) cc_final: 0.7580 (m) REVERT: C 1 MET cc_start: 0.8872 (tmm) cc_final: 0.8387 (tmm) REVERT: C 44 HIS cc_start: 0.9201 (OUTLIER) cc_final: 0.8665 (t-90) REVERT: D 61 ARG cc_start: 0.8059 (tmm-80) cc_final: 0.7441 (tmm-80) outliers start: 32 outliers final: 17 residues processed: 146 average time/residue: 0.0905 time to fit residues: 17.2033 Evaluate side-chains 131 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 553 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 195 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 18 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 HIS ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.072687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.051579 restraints weight = 32616.410| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 6.77 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7605 Z= 0.134 Angle : 0.609 7.003 10271 Z= 0.317 Chirality : 0.044 0.154 1207 Planarity : 0.003 0.032 1316 Dihedral : 4.343 17.035 1022 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.72 % Allowed : 23.61 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.27), residues: 959 helix: 0.86 (0.32), residues: 256 sheet: -0.30 (0.29), residues: 339 loop : -1.48 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 146 TYR 0.035 0.002 TYR E 408 PHE 0.015 0.001 PHE B 215 TRP 0.008 0.001 TRP C 28 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7602) covalent geometry : angle 0.60661 (10265) SS BOND : bond 0.00725 ( 3) SS BOND : angle 2.24471 ( 6) hydrogen bonds : bond 0.04032 ( 336) hydrogen bonds : angle 5.56834 ( 942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 469 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9173 (mp) REVERT: B 1 MET cc_start: 0.9142 (ppp) cc_final: 0.8268 (ppp) REVERT: B 135 CYS cc_start: 0.7991 (t) cc_final: 0.7742 (m) REVERT: C 1 MET cc_start: 0.8953 (tmm) cc_final: 0.8368 (tmm) REVERT: C 12 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8773 (tt) REVERT: C 44 HIS cc_start: 0.9256 (OUTLIER) cc_final: 0.9022 (t70) REVERT: C 61 ARG cc_start: 0.9056 (ttt-90) cc_final: 0.8650 (mtp85) REVERT: C 68 MET cc_start: 0.7034 (mpp) cc_final: 0.6657 (mpp) REVERT: C 148 CYS cc_start: 0.8989 (m) cc_final: 0.8770 (m) REVERT: C 149 ARG cc_start: 0.8543 (ttp-110) cc_final: 0.8206 (ttp80) REVERT: D 199 MET cc_start: 0.8381 (ttt) cc_final: 0.6856 (tpt) REVERT: D 249 TYR cc_start: 0.7373 (m-10) cc_final: 0.7147 (m-10) outliers start: 40 outliers final: 22 residues processed: 154 average time/residue: 0.1021 time to fit residues: 20.5125 Evaluate side-chains 138 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 553 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 2 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 195 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 389 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.072659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.051510 restraints weight = 32740.130| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 6.80 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7605 Z= 0.126 Angle : 0.600 6.186 10271 Z= 0.311 Chirality : 0.044 0.156 1207 Planarity : 0.003 0.035 1316 Dihedral : 4.251 16.513 1022 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.25 % Allowed : 24.68 % Favored : 71.07 % 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 aren not related in a simple way. whole: -0.57 (0.27), residues: 959 helix: 0.93 (0.32), residues: 258 sheet: -0.16 (0.29), residues: 332 loop : -1.47 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 146 TYR 0.039 0.002 TYR E 408 PHE 0.019 0.002 PHE E 545 TRP 0.009 0.001 TRP C 28 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7602) covalent geometry : angle 0.59850 (10265) SS BOND : bond 0.01885 ( 3) SS BOND : angle 1.85629 ( 6) hydrogen bonds : bond 0.03741 ( 336) hydrogen bonds : angle 5.24705 ( 942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9100 (ppp) cc_final: 0.8304 (ppp) REVERT: B 139 MET cc_start: 0.9403 (ttp) cc_final: 0.8970 (tmm) REVERT: B 210 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8307 (tmm-80) REVERT: C 1 MET cc_start: 0.8612 (tmm) cc_final: 0.6945 (tmm) REVERT: C 44 HIS cc_start: 0.9287 (OUTLIER) cc_final: 0.9080 (t70) REVERT: C 61 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8659 (ttt-90) REVERT: C 68 MET cc_start: 0.6939 (mpp) cc_final: 0.6553 (mpp) REVERT: C 148 CYS cc_start: 0.8990 (m) cc_final: 0.8749 (m) REVERT: C 149 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8345 (ttp-110) REVERT: D 61 ARG cc_start: 0.7808 (tmm-80) cc_final: 0.7299 (ttp80) outliers start: 36 outliers final: 25 residues processed: 145 average time/residue: 0.1031 time to fit residues: 19.2477 Evaluate side-chains 140 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 186 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 62 optimal weight: 0.4980 chunk 70 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.072558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.051448 restraints weight = 32657.736| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 6.77 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7605 Z= 0.127 Angle : 0.611 11.907 10271 Z= 0.312 Chirality : 0.044 0.160 1207 Planarity : 0.003 0.030 1316 Dihedral : 4.235 19.491 1022 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.84 % Allowed : 25.15 % Favored : 70.01 % 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 aren not related in a simple way. whole: -0.48 (0.27), residues: 959 helix: 0.99 (0.32), residues: 258 sheet: -0.10 (0.30), residues: 332 loop : -1.41 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.040 0.002 TYR E 408 PHE 0.020 0.002 PHE D 207 TRP 0.008 0.001 TRP C 28 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7602) covalent geometry : angle 0.60945 (10265) SS BOND : bond 0.00516 ( 3) SS BOND : angle 1.65024 ( 6) hydrogen bonds : bond 0.03491 ( 336) hydrogen bonds : angle 5.07930 ( 942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 LYS cc_start: 0.9131 (pptt) cc_final: 0.8889 (pptt) REVERT: E 407 PHE cc_start: 0.9043 (t80) cc_final: 0.8781 (t80) REVERT: E 415 GLN cc_start: 0.2423 (OUTLIER) cc_final: 0.2050 (tp40) REVERT: E 431 MET cc_start: 0.9454 (ptp) cc_final: 0.9153 (ptp) REVERT: E 487 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8411 (m) REVERT: E 533 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7710 (pp30) REVERT: E 554 LEU cc_start: 0.8635 (tp) cc_final: 0.8347 (pp) REVERT: B 1 MET cc_start: 0.9088 (ppp) cc_final: 0.8321 (ppp) REVERT: B 40 MET cc_start: 0.7766 (tmm) cc_final: 0.7417 (tmm) REVERT: B 135 CYS cc_start: 0.8084 (t) cc_final: 0.7605 (m) REVERT: B 199 MET cc_start: 0.6436 (ttp) cc_final: 0.5975 (ttp) REVERT: C 1 MET cc_start: 0.8638 (tmm) cc_final: 0.7232 (tmm) REVERT: C 61 ARG cc_start: 0.9106 (ttt-90) cc_final: 0.8698 (ttt-90) REVERT: C 148 CYS cc_start: 0.8985 (m) cc_final: 0.8722 (m) outliers start: 41 outliers final: 29 residues processed: 150 average time/residue: 0.0978 time to fit residues: 19.1468 Evaluate side-chains 142 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 415 GLN Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 533 GLN Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 92 optimal weight: 0.0980 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 83 optimal weight: 6.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.071735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.050428 restraints weight = 32443.883| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 6.73 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7605 Z= 0.157 Angle : 0.623 9.261 10271 Z= 0.318 Chirality : 0.044 0.147 1207 Planarity : 0.003 0.032 1316 Dihedral : 4.288 17.313 1022 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.08 % Allowed : 25.50 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.27), residues: 959 helix: 0.88 (0.32), residues: 260 sheet: -0.08 (0.30), residues: 328 loop : -1.41 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.039 0.002 TYR E 408 PHE 0.019 0.002 PHE B 2 TRP 0.009 0.001 TRP C 28 HIS 0.003 0.001 HIS E 485 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7602) covalent geometry : angle 0.62196 (10265) SS BOND : bond 0.00528 ( 3) SS BOND : angle 1.60071 ( 6) hydrogen bonds : bond 0.03589 ( 336) hydrogen bonds : angle 5.07310 ( 942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 LYS cc_start: 0.9151 (pptt) cc_final: 0.8921 (pptt) REVERT: E 487 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8357 (m) REVERT: E 498 ASP cc_start: 0.9228 (p0) cc_final: 0.8819 (p0) REVERT: E 542 ARG cc_start: 0.8954 (ttm-80) cc_final: 0.8720 (ttm-80) REVERT: E 554 LEU cc_start: 0.8558 (tp) cc_final: 0.8310 (pp) REVERT: B 1 MET cc_start: 0.9088 (ppp) cc_final: 0.8763 (ppp) REVERT: B 20 LYS cc_start: 0.9618 (tttt) cc_final: 0.9349 (tttp) REVERT: B 40 MET cc_start: 0.7810 (tmm) cc_final: 0.7496 (tmm) REVERT: B 135 CYS cc_start: 0.8176 (t) cc_final: 0.7756 (m) REVERT: B 139 MET cc_start: 0.9387 (ttp) cc_final: 0.8968 (tmm) REVERT: B 199 MET cc_start: 0.6431 (ttp) cc_final: 0.6070 (ttp) REVERT: C 1 MET cc_start: 0.8574 (tmm) cc_final: 0.7237 (tmm) REVERT: C 61 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8651 (ttt-90) REVERT: C 149 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.8067 (ptt90) REVERT: D 1 MET cc_start: 0.8967 (tpt) cc_final: 0.8646 (tpt) REVERT: D 61 ARG cc_start: 0.8104 (tmm-80) cc_final: 0.7576 (tmm-80) REVERT: D 64 ARG cc_start: 0.9132 (tmm160) cc_final: 0.8863 (tmm-80) REVERT: D 249 TYR cc_start: 0.8050 (m-10) cc_final: 0.7834 (m-10) outliers start: 43 outliers final: 32 residues processed: 139 average time/residue: 0.0993 time to fit residues: 18.3725 Evaluate side-chains 143 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 553 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.068955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.047452 restraints weight = 33215.482| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 6.61 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 7605 Z= 0.327 Angle : 0.741 7.698 10271 Z= 0.388 Chirality : 0.047 0.193 1207 Planarity : 0.004 0.033 1316 Dihedral : 4.906 22.273 1022 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.31 % Allowed : 25.50 % Favored : 69.19 % 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 aren not related in a simple way. whole: -0.81 (0.27), residues: 959 helix: 0.43 (0.31), residues: 261 sheet: -0.19 (0.31), residues: 301 loop : -1.41 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 210 TYR 0.039 0.003 TYR E 408 PHE 0.025 0.003 PHE D 215 TRP 0.017 0.003 TRP C 28 HIS 0.009 0.002 HIS E 507 Details of bonding type rmsd covalent geometry : bond 0.00700 ( 7602) covalent geometry : angle 0.74008 (10265) SS BOND : bond 0.00749 ( 3) SS BOND : angle 2.02878 ( 6) hydrogen bonds : bond 0.04348 ( 336) hydrogen bonds : angle 5.61271 ( 942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 407 PHE cc_start: 0.9119 (t80) cc_final: 0.8789 (t80) REVERT: E 415 GLN cc_start: 0.2900 (OUTLIER) cc_final: 0.2231 (tp40) REVERT: E 487 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8350 (m) REVERT: E 498 ASP cc_start: 0.9280 (p0) cc_final: 0.8848 (p0) REVERT: E 500 PHE cc_start: 0.9428 (m-80) cc_final: 0.9166 (m-80) REVERT: E 533 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8131 (pp30) REVERT: E 554 LEU cc_start: 0.8611 (tp) cc_final: 0.8322 (pp) REVERT: B 1 MET cc_start: 0.9118 (ppp) cc_final: 0.8842 (ppp) REVERT: B 20 LYS cc_start: 0.9554 (tttt) cc_final: 0.9121 (mtpp) REVERT: B 40 MET cc_start: 0.7825 (tmm) cc_final: 0.7465 (tmm) REVERT: B 135 CYS cc_start: 0.8240 (t) cc_final: 0.7827 (m) REVERT: B 199 MET cc_start: 0.6549 (ttp) cc_final: 0.6228 (ttp) REVERT: C 28 TRP cc_start: 0.8523 (m100) cc_final: 0.7714 (m-90) REVERT: C 52 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8946 (tt) REVERT: C 148 CYS cc_start: 0.8993 (m) cc_final: 0.8772 (m) REVERT: D 1 MET cc_start: 0.9016 (tpt) cc_final: 0.8804 (tpp) REVERT: D 249 TYR cc_start: 0.8473 (m-80) cc_final: 0.8117 (m-10) outliers start: 45 outliers final: 31 residues processed: 144 average time/residue: 0.0934 time to fit residues: 17.7775 Evaluate side-chains 139 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 415 GLN Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 533 GLN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 61 ARG Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 0.0270 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.070142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049019 restraints weight = 33346.371| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 6.69 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7605 Z= 0.196 Angle : 0.683 8.631 10271 Z= 0.351 Chirality : 0.046 0.265 1207 Planarity : 0.003 0.029 1316 Dihedral : 4.652 18.154 1022 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.55 % Allowed : 27.04 % Favored : 67.41 % 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 aren not related in a simple way. whole: -0.76 (0.27), residues: 959 helix: 0.48 (0.31), residues: 259 sheet: -0.16 (0.30), residues: 317 loop : -1.42 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 61 TYR 0.041 0.002 TYR E 408 PHE 0.021 0.002 PHE B 215 TRP 0.014 0.002 TRP C 28 HIS 0.003 0.001 HIS E 485 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7602) covalent geometry : angle 0.68113 (10265) SS BOND : bond 0.00765 ( 3) SS BOND : angle 2.31690 ( 6) hydrogen bonds : bond 0.03892 ( 336) hydrogen bonds : angle 5.38200 ( 942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 487 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8380 (m) REVERT: E 498 ASP cc_start: 0.9245 (p0) cc_final: 0.8796 (p0) REVERT: E 500 PHE cc_start: 0.9377 (m-80) cc_final: 0.9131 (m-80) REVERT: E 533 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8178 (pp30) REVERT: E 542 ARG cc_start: 0.8994 (ttm-80) cc_final: 0.8730 (ttm170) REVERT: E 554 LEU cc_start: 0.8617 (tp) cc_final: 0.8391 (pp) REVERT: B 1 MET cc_start: 0.9182 (ppp) cc_final: 0.8898 (ppp) REVERT: B 40 MET cc_start: 0.7828 (tmm) cc_final: 0.7461 (tmm) REVERT: B 121 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8344 (mm) REVERT: B 135 CYS cc_start: 0.8139 (t) cc_final: 0.7913 (m) REVERT: C 28 TRP cc_start: 0.8485 (m100) cc_final: 0.7751 (m-90) REVERT: C 148 CYS cc_start: 0.9004 (m) cc_final: 0.8786 (m) REVERT: D 64 ARG cc_start: 0.9312 (tmm160) cc_final: 0.8986 (tmm-80) REVERT: D 249 TYR cc_start: 0.8270 (m-80) cc_final: 0.7995 (m-10) outliers start: 47 outliers final: 37 residues processed: 147 average time/residue: 0.0976 time to fit residues: 18.9038 Evaluate side-chains 146 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 455 PHE Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 533 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 2 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 0.3980 chunk 9 optimal weight: 0.0370 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.071561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050293 restraints weight = 32596.396| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 6.78 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7605 Z= 0.131 Angle : 0.673 11.114 10271 Z= 0.336 Chirality : 0.045 0.206 1207 Planarity : 0.003 0.030 1316 Dihedral : 4.383 16.354 1022 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.60 % Allowed : 27.51 % Favored : 67.89 % 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 aren not related in a simple way. whole: -0.64 (0.27), residues: 959 helix: 0.70 (0.32), residues: 258 sheet: -0.22 (0.30), residues: 320 loop : -1.30 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 210 TYR 0.041 0.002 TYR E 408 PHE 0.020 0.002 PHE E 552 TRP 0.011 0.001 TRP C 28 HIS 0.002 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7602) covalent geometry : angle 0.67233 (10265) SS BOND : bond 0.00325 ( 3) SS BOND : angle 1.56046 ( 6) hydrogen bonds : bond 0.03563 ( 336) hydrogen bonds : angle 5.14072 ( 942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 487 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8377 (m) REVERT: E 498 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.8839 (p0) REVERT: E 533 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8295 (pp30) REVERT: E 542 ARG cc_start: 0.8948 (ttm-80) cc_final: 0.8675 (ttm170) REVERT: B 1 MET cc_start: 0.9203 (ppp) cc_final: 0.8929 (ppp) REVERT: B 20 LYS cc_start: 0.9598 (tttt) cc_final: 0.9083 (mtpp) REVERT: B 40 MET cc_start: 0.7793 (tmm) cc_final: 0.7454 (tmm) REVERT: B 244 MET cc_start: 0.9134 (tpp) cc_final: 0.8842 (tpp) REVERT: C 61 ARG cc_start: 0.9167 (mtp85) cc_final: 0.8710 (ptm-80) REVERT: C 148 CYS cc_start: 0.9022 (m) cc_final: 0.8813 (m) REVERT: C 149 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.8078 (ptt90) REVERT: D 64 ARG cc_start: 0.9215 (tmm160) cc_final: 0.8897 (tmm-80) REVERT: D 229 MET cc_start: 0.9137 (pmm) cc_final: 0.8806 (pmm) outliers start: 39 outliers final: 35 residues processed: 143 average time/residue: 0.1062 time to fit residues: 19.7544 Evaluate side-chains 148 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 533 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 2 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 chunk 85 optimal weight: 0.0010 chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 32 optimal weight: 7.9990 overall best weight: 2.0948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.071295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.050095 restraints weight = 33101.054| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 6.78 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7605 Z= 0.150 Angle : 0.690 10.055 10271 Z= 0.345 Chirality : 0.045 0.194 1207 Planarity : 0.003 0.029 1316 Dihedral : 4.371 17.106 1022 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.13 % Allowed : 27.98 % Favored : 67.89 % 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 aren not related in a simple way. whole: -0.61 (0.27), residues: 959 helix: 0.65 (0.32), residues: 262 sheet: -0.10 (0.31), residues: 314 loop : -1.34 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.041 0.002 TYR E 408 PHE 0.019 0.002 PHE E 552 TRP 0.014 0.001 TRP C 28 HIS 0.002 0.001 HIS E 485 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7602) covalent geometry : angle 0.68896 (10265) SS BOND : bond 0.00635 ( 3) SS BOND : angle 1.87201 ( 6) hydrogen bonds : bond 0.03582 ( 336) hydrogen bonds : angle 5.14065 ( 942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 487 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8305 (m) REVERT: E 498 ASP cc_start: 0.9266 (p0) cc_final: 0.8835 (p0) REVERT: E 500 PHE cc_start: 0.9359 (m-80) cc_final: 0.9104 (m-80) REVERT: E 533 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8348 (pp30) REVERT: E 542 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8655 (ttm170) REVERT: B 1 MET cc_start: 0.9153 (ppp) cc_final: 0.8876 (ppp) REVERT: B 20 LYS cc_start: 0.9591 (tttt) cc_final: 0.9075 (mtpp) REVERT: B 40 MET cc_start: 0.7808 (tmm) cc_final: 0.7483 (tmm) REVERT: B 121 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 139 MET cc_start: 0.9357 (ttp) cc_final: 0.8921 (tmm) REVERT: C 148 CYS cc_start: 0.9027 (m) cc_final: 0.8809 (m) REVERT: C 149 ARG cc_start: 0.8517 (ttp-110) cc_final: 0.8083 (ptt90) REVERT: C 210 ARG cc_start: 0.8607 (ptt180) cc_final: 0.8376 (ptt180) REVERT: D 64 ARG cc_start: 0.9229 (tmm160) cc_final: 0.8859 (tmm-80) REVERT: D 66 LEU cc_start: 0.9084 (tp) cc_final: 0.8821 (tt) REVERT: D 199 MET cc_start: 0.7847 (ttt) cc_final: 0.7513 (ttt) REVERT: D 229 MET cc_start: 0.9201 (pmm) cc_final: 0.8827 (pmm) outliers start: 35 outliers final: 30 residues processed: 138 average time/residue: 0.1019 time to fit residues: 18.2692 Evaluate side-chains 143 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 372 HIS Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 533 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 246 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.070145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.048923 restraints weight = 32781.297| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 6.68 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7605 Z= 0.203 Angle : 0.717 10.827 10271 Z= 0.361 Chirality : 0.045 0.194 1207 Planarity : 0.003 0.031 1316 Dihedral : 4.548 18.782 1022 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.01 % Allowed : 27.98 % Favored : 68.00 % 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 aren not related in a simple way. whole: -0.70 (0.27), residues: 959 helix: 0.59 (0.32), residues: 262 sheet: -0.12 (0.32), residues: 294 loop : -1.38 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 61 TYR 0.041 0.002 TYR E 408 PHE 0.026 0.003 PHE B 207 TRP 0.011 0.002 TRP C 28 HIS 0.003 0.001 HIS E 485 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 7602) covalent geometry : angle 0.71556 (10265) SS BOND : bond 0.00752 ( 3) SS BOND : angle 1.68977 ( 6) hydrogen bonds : bond 0.03770 ( 336) hydrogen bonds : angle 5.32864 ( 942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1740.93 seconds wall clock time: 30 minutes 42.74 seconds (1842.74 seconds total)