Starting phenix.real_space_refine on Mon Apr 28 11:43:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chm_45590/04_2025/9chm_45590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chm_45590/04_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_45590/04_2025/9chm_45590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chm_45590/04_2025/9chm_45590.map" model { file = "/net/cci-nas-00/data/ceres_data/9chm_45590/04_2025/9chm_45590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chm_45590/04_2025/9chm_45590.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.10, per 1000 atoms: 0.68 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: 1.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.10 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: 2.32 Time building geometry restraints manager: 2.21 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: 1.070 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.920 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (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 TRP 0.008 0.001 TRP E 428 HIS 0.007 0.001 HIS B 246 PHE 0.028 0.002 PHE B 2 TYR 0.041 0.002 TYR E 408 ARG 0.009 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.27452 ( 336) hydrogen bonds : angle 9.11428 ( 942) SS BOND : bond 0.00582 ( 3) SS BOND : angle 2.56568 ( 6) covalent geometry : bond 0.00389 ( 7602) covalent geometry : angle 0.81982 (10265) *********************** 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 : 1.017 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: 0.2349 time to fit residues: 36.7869 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 : 0.874 ------------------------------------------------------------------------------- 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 81 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ** 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 = 0.3623 r_free = 0.3623 target = 0.072239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050912 restraints weight = 32536.341| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 6.74 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1715 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= 0.182 Angle : 0.686 8.202 10271 Z= 0.356 Chirality : 0.045 0.150 1207 Planarity : 0.004 0.045 1316 Dihedral : 4.643 20.934 1024 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.54 % Allowed : 24.68 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.27), residues: 959 helix: 0.83 (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 TRP 0.013 0.002 TRP C 28 HIS 0.004 0.001 HIS E 372 PHE 0.015 0.002 PHE E 545 TYR 0.038 0.003 TYR E 408 ARG 0.007 0.001 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 336) hydrogen bonds : angle 6.22427 ( 942) SS BOND : bond 0.01552 ( 3) SS BOND : angle 3.24535 ( 6) covalent geometry : bond 0.00390 ( 7602) covalent geometry : angle 0.68167 (10265) *********************** 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 155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 431 MET cc_start: 0.9486 (ptp) cc_final: 0.9185 (ppp) REVERT: B 135 CYS cc_start: 0.7898 (t) cc_final: 0.7612 (m) REVERT: C 1 MET cc_start: 0.8893 (tmm) cc_final: 0.8463 (tmm) REVERT: C 44 HIS cc_start: 0.9194 (OUTLIER) cc_final: 0.8740 (t70) REVERT: D 61 ARG cc_start: 0.8118 (tmm-80) cc_final: 0.7884 (tmm-80) outliers start: 30 outliers final: 18 residues processed: 146 average time/residue: 0.2247 time to fit residues: 43.2077 Evaluate side-chains 134 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 448 GLU Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain B residue 12 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 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 33 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.069884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048526 restraints weight = 33347.482| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 6.67 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7605 Z= 0.270 Angle : 0.693 6.460 10271 Z= 0.365 Chirality : 0.046 0.144 1207 Planarity : 0.004 0.035 1316 Dihedral : 4.830 21.673 1022 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.31 % Allowed : 24.20 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.27), residues: 959 helix: 0.52 (0.32), residues: 261 sheet: -0.50 (0.28), residues: 335 loop : -1.55 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 512 HIS 0.005 0.001 HIS E 485 PHE 0.020 0.002 PHE D 215 TYR 0.034 0.003 TYR E 408 ARG 0.004 0.001 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 336) hydrogen bonds : angle 5.95214 ( 942) SS BOND : bond 0.00683 ( 3) SS BOND : angle 2.54846 ( 6) covalent geometry : bond 0.00585 ( 7602) covalent geometry : angle 0.69011 (10265) *********************** 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 161 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 LYS cc_start: 0.9191 (pptt) cc_final: 0.8966 (pptt) REVERT: E 498 ASP cc_start: 0.9206 (p0) cc_final: 0.8938 (p0) REVERT: B 1 MET cc_start: 0.9174 (ppp) cc_final: 0.8254 (ppp) REVERT: B 244 MET cc_start: 0.9109 (tpp) cc_final: 0.8869 (tpt) REVERT: C 12 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8843 (tt) REVERT: C 28 TRP cc_start: 0.8344 (m100) cc_final: 0.7719 (m-90) REVERT: C 44 HIS cc_start: 0.9273 (OUTLIER) cc_final: 0.8926 (t-90) REVERT: C 52 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8891 (tt) REVERT: D 61 ARG cc_start: 0.7955 (tmm-80) cc_final: 0.7609 (tmm-80) REVERT: D 112 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7636 (p) outliers start: 45 outliers final: 29 residues processed: 147 average time/residue: 0.2256 time to fit residues: 43.1137 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 : 0.855 ------------------------------------------------------------------------------- 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 68 MET 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 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 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 2 PHE Chi-restraints excluded: chain D residue 37 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 112 SER Chi-restraints excluded: chain D residue 186 SER 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 60 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 83 optimal weight: 0.0570 chunk 42 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 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 = 0.3605 r_free = 0.3605 target = 0.071208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.050016 restraints weight = 32556.867| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 6.70 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7605 Z= 0.138 Angle : 0.605 8.146 10271 Z= 0.313 Chirality : 0.044 0.146 1207 Planarity : 0.003 0.030 1316 Dihedral : 4.447 16.498 1022 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.96 % Allowed : 24.79 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 959 helix: 0.84 (0.33), residues: 257 sheet: -0.42 (0.29), residues: 334 loop : -1.45 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 28 HIS 0.005 0.001 HIS C 44 PHE 0.017 0.002 PHE D 207 TYR 0.036 0.002 TYR E 408 ARG 0.005 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 336) hydrogen bonds : angle 5.34730 ( 942) SS BOND : bond 0.00492 ( 3) SS BOND : angle 1.96325 ( 6) covalent geometry : bond 0.00301 ( 7602) covalent geometry : angle 0.60365 (10265) *********************** 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 169 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 384 LYS cc_start: 0.9172 (pptt) cc_final: 0.8935 (pptt) REVERT: E 469 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9192 (mp) REVERT: E 487 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8448 (m) REVERT: E 498 ASP cc_start: 0.9233 (p0) cc_final: 0.8932 (p0) REVERT: B 1 MET cc_start: 0.9164 (ppp) cc_final: 0.8311 (ppp) REVERT: B 68 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7720 (pmm) REVERT: B 135 CYS cc_start: 0.8258 (t) cc_final: 0.7884 (m) REVERT: B 139 MET cc_start: 0.9418 (ttp) cc_final: 0.8980 (tmm) REVERT: B 244 MET cc_start: 0.9092 (tpp) cc_final: 0.8825 (tpt) REVERT: C 2 PHE cc_start: 0.8956 (t80) cc_final: 0.8684 (t80) REVERT: C 12 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8663 (tt) REVERT: C 28 TRP cc_start: 0.8294 (m100) cc_final: 0.7868 (m-90) REVERT: C 44 HIS cc_start: 0.9267 (OUTLIER) cc_final: 0.9042 (t70) REVERT: C 61 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8806 (mtp85) REVERT: C 149 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.8213 (ttp80) REVERT: D 1 MET cc_start: 0.8601 (tpt) cc_final: 0.8344 (tpt) REVERT: D 61 ARG cc_start: 0.8120 (tmm-80) cc_final: 0.7734 (tmm-80) outliers start: 42 outliers final: 20 residues processed: 159 average time/residue: 0.2554 time to fit residues: 52.5020 Evaluate side-chains 138 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 415 GLN 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 487 VAL 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 68 MET 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 224 THR Chi-restraints excluded: chain C residue 12 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 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 261 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3586 r_free = 0.3586 target = 0.070356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.048858 restraints weight = 32525.662| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 6.68 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3110 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= 0.207 Angle : 0.651 10.807 10271 Z= 0.336 Chirality : 0.044 0.168 1207 Planarity : 0.003 0.029 1316 Dihedral : 4.554 19.624 1022 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.67 % Allowed : 25.62 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 959 helix: 0.78 (0.32), residues: 259 sheet: -0.32 (0.29), residues: 324 loop : -1.46 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 28 HIS 0.005 0.001 HIS C 44 PHE 0.020 0.002 PHE D 207 TYR 0.037 0.002 TYR E 408 ARG 0.004 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 336) hydrogen bonds : angle 5.36708 ( 942) SS BOND : bond 0.00573 ( 3) SS BOND : angle 1.95832 ( 6) covalent geometry : bond 0.00447 ( 7602) covalent geometry : angle 0.64915 (10265) *********************** 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 160 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.857 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 384 LYS cc_start: 0.9187 (pptt) cc_final: 0.8962 (pptt) REVERT: E 469 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9216 (mp) REVERT: E 487 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8422 (m) REVERT: E 498 ASP cc_start: 0.9245 (p0) cc_final: 0.8920 (p0) REVERT: E 500 PHE cc_start: 0.9284 (m-80) cc_final: 0.9056 (m-80) REVERT: E 542 ARG cc_start: 0.8936 (ttm170) cc_final: 0.8631 (ttm-80) REVERT: B 1 MET cc_start: 0.9147 (ppp) cc_final: 0.8336 (ppp) REVERT: B 20 LYS cc_start: 0.9565 (tttt) cc_final: 0.9148 (mtpp) REVERT: B 68 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7593 (pmm) REVERT: B 135 CYS cc_start: 0.8289 (t) cc_final: 0.7764 (m) REVERT: B 199 MET cc_start: 0.6578 (ttp) cc_final: 0.6162 (ttp) REVERT: B 244 MET cc_start: 0.9087 (tpp) cc_final: 0.8777 (tpt) REVERT: C 12 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8775 (tt) REVERT: C 28 TRP cc_start: 0.8377 (m100) cc_final: 0.7851 (m-90) REVERT: C 44 HIS cc_start: 0.9250 (OUTLIER) cc_final: 0.8885 (t70) REVERT: C 149 ARG cc_start: 0.8557 (ttp-110) cc_final: 0.8133 (ptm-80) REVERT: C 249 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: D 64 ARG cc_start: 0.9492 (tmt170) cc_final: 0.9202 (tmm-80) REVERT: D 112 SER cc_start: 0.7889 (OUTLIER) cc_final: 0.7585 (p) REVERT: D 249 TYR cc_start: 0.8268 (m-80) cc_final: 0.8001 (m-10) outliers start: 48 outliers final: 34 residues processed: 149 average time/residue: 0.2180 time to fit residues: 42.2371 Evaluate side-chains 148 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 469 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 550 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 68 MET 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 209 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 39 SER 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 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 249 TYR 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 112 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 62 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3631 r_free = 0.3631 target = 0.072300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051277 restraints weight = 32308.846| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 6.79 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7605 Z= 0.109 Angle : 0.615 9.930 10271 Z= 0.311 Chirality : 0.044 0.147 1207 Planarity : 0.003 0.029 1316 Dihedral : 4.248 15.331 1022 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.25 % Allowed : 25.97 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.27), residues: 959 helix: 0.90 (0.32), residues: 259 sheet: -0.25 (0.30), residues: 324 loop : -1.39 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 28 HIS 0.002 0.000 HIS C 44 PHE 0.019 0.001 PHE D 207 TYR 0.037 0.002 TYR E 408 ARG 0.005 0.000 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 336) hydrogen bonds : angle 5.02553 ( 942) SS BOND : bond 0.00344 ( 3) SS BOND : angle 1.52168 ( 6) covalent geometry : bond 0.00233 ( 7602) covalent geometry : angle 0.61380 (10265) *********************** 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 163 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 469 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9158 (mp) REVERT: E 487 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8363 (m) REVERT: E 498 ASP cc_start: 0.9236 (p0) cc_final: 0.8901 (p0) REVERT: E 533 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8033 (pp30) REVERT: E 542 ARG cc_start: 0.8862 (ttm170) cc_final: 0.8566 (ttm-80) REVERT: B 1 MET cc_start: 0.9152 (ppp) cc_final: 0.8791 (ppp) REVERT: B 40 MET cc_start: 0.7696 (tmm) cc_final: 0.7390 (tmm) REVERT: B 135 CYS cc_start: 0.8274 (t) cc_final: 0.7954 (m) REVERT: B 139 MET cc_start: 0.9375 (ttp) cc_final: 0.8961 (tmm) REVERT: B 244 MET cc_start: 0.9084 (tpp) cc_final: 0.8810 (tpt) REVERT: C 12 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8732 (tt) REVERT: C 28 TRP cc_start: 0.8265 (m100) cc_final: 0.7599 (m-90) REVERT: C 44 HIS cc_start: 0.9314 (OUTLIER) cc_final: 0.9039 (t70) REVERT: D 61 ARG cc_start: 0.7912 (tmm-80) cc_final: 0.7556 (ttp80) REVERT: D 64 ARG cc_start: 0.9424 (tmt170) cc_final: 0.9176 (tmm-80) REVERT: D 229 MET cc_start: 0.9160 (pmm) cc_final: 0.8894 (pmm) REVERT: D 249 TYR cc_start: 0.7990 (m-80) cc_final: 0.7735 (m-10) outliers start: 36 outliers final: 25 residues processed: 153 average time/residue: 0.2350 time to fit residues: 46.7844 Evaluate side-chains 144 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 469 LEU Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 506 GLN 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 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 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 44 HIS 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 102 VAL 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 10 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3604 r_free = 0.3604 target = 0.070958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050095 restraints weight = 32062.446| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 6.64 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7605 Z= 0.165 Angle : 0.649 11.625 10271 Z= 0.330 Chirality : 0.044 0.174 1207 Planarity : 0.003 0.030 1316 Dihedral : 4.311 17.671 1022 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.19 % Allowed : 26.45 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.27), residues: 959 helix: 0.96 (0.32), residues: 258 sheet: -0.20 (0.30), residues: 324 loop : -1.43 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 512 HIS 0.005 0.001 HIS E 507 PHE 0.016 0.002 PHE E 545 TYR 0.037 0.002 TYR E 408 ARG 0.006 0.001 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 336) hydrogen bonds : angle 5.07614 ( 942) SS BOND : bond 0.00599 ( 3) SS BOND : angle 2.29154 ( 6) covalent geometry : bond 0.00364 ( 7602) covalent geometry : angle 0.64700 (10265) *********************** 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 159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 469 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9191 (mp) REVERT: E 498 ASP cc_start: 0.9259 (p0) cc_final: 0.8923 (p0) REVERT: E 500 PHE cc_start: 0.9310 (m-80) cc_final: 0.9031 (m-80) REVERT: B 1 MET cc_start: 0.9124 (ppp) cc_final: 0.8784 (ppp) REVERT: B 40 MET cc_start: 0.7696 (tmm) cc_final: 0.7427 (tmm) REVERT: B 244 MET cc_start: 0.9060 (tpp) cc_final: 0.8746 (tpt) REVERT: C 12 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8742 (tt) REVERT: C 44 HIS cc_start: 0.9279 (OUTLIER) cc_final: 0.8943 (t70) REVERT: D 61 ARG cc_start: 0.7965 (tmm-80) cc_final: 0.7732 (ttp80) REVERT: D 112 SER cc_start: 0.7847 (OUTLIER) cc_final: 0.7562 (p) REVERT: D 249 TYR cc_start: 0.8290 (m-80) cc_final: 0.7987 (m-10) outliers start: 44 outliers final: 32 residues processed: 151 average time/residue: 0.2155 time to fit residues: 42.7478 Evaluate side-chains 144 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 469 LEU Chi-restraints excluded: chain E residue 479 SER Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE 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 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 39 SER 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 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 112 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 58 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 50.0000 chunk 85 optimal weight: 7.9990 chunk 66 optimal weight: 0.0770 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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 49 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 = 0.3662 r_free = 0.3662 target = 0.072967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.051485 restraints weight = 33081.040| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 6.94 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3830 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= 0.116 Angle : 0.656 11.378 10271 Z= 0.329 Chirality : 0.045 0.243 1207 Planarity : 0.003 0.031 1316 Dihedral : 4.214 16.624 1022 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.01 % Allowed : 27.86 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 959 helix: 0.74 (0.32), residues: 259 sheet: -0.19 (0.30), residues: 322 loop : -1.37 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 28 HIS 0.004 0.001 HIS C 44 PHE 0.017 0.001 PHE D 207 TYR 0.038 0.002 TYR E 408 ARG 0.005 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 336) hydrogen bonds : angle 4.87804 ( 942) SS BOND : bond 0.00488 ( 3) SS BOND : angle 1.82072 ( 6) covalent geometry : bond 0.00254 ( 7602) covalent geometry : angle 0.65474 (10265) *********************** 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 151 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 415 GLN cc_start: 0.2925 (OUTLIER) cc_final: 0.2576 (mm-40) REVERT: E 469 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9180 (mp) REVERT: E 487 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8697 (m) REVERT: E 498 ASP cc_start: 0.9266 (p0) cc_final: 0.8818 (p0) REVERT: B 1 MET cc_start: 0.9157 (ppp) cc_final: 0.8806 (ppp) REVERT: B 40 MET cc_start: 0.7765 (tmm) cc_final: 0.7508 (tmm) REVERT: B 135 CYS cc_start: 0.8278 (t) cc_final: 0.7940 (m) REVERT: B 244 MET cc_start: 0.9051 (tpp) cc_final: 0.8798 (tpt) REVERT: C 12 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8720 (tt) REVERT: D 61 ARG cc_start: 0.8008 (tmm-80) cc_final: 0.7728 (ttp80) REVERT: D 249 TYR cc_start: 0.8032 (m-80) cc_final: 0.7815 (m-10) outliers start: 34 outliers final: 24 residues processed: 145 average time/residue: 0.2344 time to fit residues: 44.3129 Evaluate side-chains 142 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 469 LEU Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 514 LYS 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 137 VAL 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 12 LEU Chi-restraints excluded: chain C residue 21 ASP 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 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 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 68 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN C 44 HIS ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 HIS ** 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 = 0.3678 r_free = 0.3678 target = 0.073650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052597 restraints weight = 33117.084| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 6.86 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7605 Z= 0.115 Angle : 0.663 11.296 10271 Z= 0.331 Chirality : 0.045 0.193 1207 Planarity : 0.003 0.039 1316 Dihedral : 4.156 19.540 1020 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.42 % Allowed : 28.34 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.27), residues: 959 helix: 0.70 (0.32), residues: 259 sheet: -0.06 (0.30), residues: 318 loop : -1.39 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 28 HIS 0.002 0.000 HIS E 507 PHE 0.017 0.001 PHE D 207 TYR 0.040 0.002 TYR E 408 ARG 0.005 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 336) hydrogen bonds : angle 4.85031 ( 942) SS BOND : bond 0.00399 ( 3) SS BOND : angle 1.87306 ( 6) covalent geometry : bond 0.00254 ( 7602) covalent geometry : angle 0.66120 (10265) *********************** 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 146 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 396 PHE cc_start: 0.8366 (m-80) cc_final: 0.8106 (t80) REVERT: E 469 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9246 (mp) REVERT: E 487 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8684 (m) REVERT: E 498 ASP cc_start: 0.9239 (p0) cc_final: 0.8823 (p0) REVERT: B 1 MET cc_start: 0.9197 (ppp) cc_final: 0.8835 (ppp) REVERT: B 40 MET cc_start: 0.7854 (tmm) cc_final: 0.7575 (tmm) REVERT: B 135 CYS cc_start: 0.8211 (t) cc_final: 0.7949 (m) REVERT: B 244 MET cc_start: 0.8967 (tpp) cc_final: 0.8754 (tpt) REVERT: C 12 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8781 (tt) REVERT: D 64 ARG cc_start: 0.9308 (tmm-80) cc_final: 0.9072 (tmm160) outliers start: 29 outliers final: 24 residues processed: 141 average time/residue: 0.2273 time to fit residues: 41.9225 Evaluate side-chains 143 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE 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 112 SER 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 224 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 39 SER 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 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 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 67 optimal weight: 0.5980 chunk 79 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 56 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 87 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 HIS ** 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 = 0.3657 r_free = 0.3657 target = 0.072627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051156 restraints weight = 32897.567| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 6.91 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4130 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= 0.138 Angle : 0.667 10.204 10271 Z= 0.336 Chirality : 0.044 0.169 1207 Planarity : 0.003 0.040 1316 Dihedral : 4.284 19.466 1020 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.66 % Allowed : 28.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.27), residues: 959 helix: 0.65 (0.32), residues: 260 sheet: -0.09 (0.31), residues: 316 loop : -1.40 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 28 HIS 0.006 0.001 HIS C 44 PHE 0.018 0.002 PHE E 545 TYR 0.041 0.002 TYR E 408 ARG 0.006 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 336) hydrogen bonds : angle 4.93219 ( 942) SS BOND : bond 0.00556 ( 3) SS BOND : angle 1.72979 ( 6) covalent geometry : bond 0.00307 ( 7602) covalent geometry : angle 0.66559 (10265) ********************** 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 144 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 396 PHE cc_start: 0.8411 (m-80) cc_final: 0.8063 (t80) REVERT: E 469 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9178 (mp) REVERT: E 487 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8653 (m) REVERT: E 498 ASP cc_start: 0.9287 (p0) cc_final: 0.8897 (p0) REVERT: B 1 MET cc_start: 0.9160 (ppp) cc_final: 0.8817 (ppp) REVERT: B 40 MET cc_start: 0.7856 (tmm) cc_final: 0.7539 (tmm) REVERT: B 135 CYS cc_start: 0.8412 (t) cc_final: 0.8068 (m) REVERT: B 244 MET cc_start: 0.9028 (tpp) cc_final: 0.8769 (tpt) REVERT: C 12 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8761 (tt) REVERT: D 61 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7049 (ttp80) outliers start: 31 outliers final: 24 residues processed: 137 average time/residue: 0.2233 time to fit residues: 40.1610 Evaluate side-chains 139 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 455 PHE Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 506 GLN Chi-restraints excluded: chain E residue 514 LYS Chi-restraints excluded: chain E residue 519 ILE 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 112 SER 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 224 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 39 SER 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 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 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 82 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 HIS ** 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 = 0.3648 r_free = 0.3648 target = 0.072151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050781 restraints weight = 32520.814| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 6.82 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7605 Z= 0.153 Angle : 0.688 10.100 10271 Z= 0.343 Chirality : 0.044 0.154 1207 Planarity : 0.004 0.058 1316 Dihedral : 4.293 18.478 1020 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.78 % Allowed : 28.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 959 helix: 0.58 (0.33), residues: 260 sheet: -0.27 (0.31), residues: 316 loop : -1.32 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 28 HIS 0.005 0.001 HIS C 44 PHE 0.025 0.002 PHE B 207 TYR 0.040 0.002 TYR E 408 ARG 0.007 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 336) hydrogen bonds : angle 4.99946 ( 942) SS BOND : bond 0.00544 ( 3) SS BOND : angle 2.04129 ( 6) covalent geometry : bond 0.00340 ( 7602) covalent geometry : angle 0.68613 (10265) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3724.10 seconds wall clock time: 64 minutes 45.41 seconds (3885.41 seconds total)