Starting phenix.real_space_refine on Wed Mar 12 07:02:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chm_45590/03_2025/9chm_45590.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chm_45590/03_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_45590/03_2025/9chm_45590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chm_45590/03_2025/9chm_45590.map" model { file = "/net/cci-nas-00/data/ceres_data/9chm_45590/03_2025/9chm_45590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chm_45590/03_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-5624/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: 5.32, per 1000 atoms: 0.71 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: 2.09 Conformation dependent library (CDL) restraints added in 1.3 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: 1.03 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: 2.42 Time building geometry restraints manager: 2.41 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: 2.120 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: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.220 Find NCS groups from input model: 0.220 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- 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 7602 Z= 0.256 Angle : 0.820 10.922 10265 Z= 0.440 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.978 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: 0.2343 time to fit residues: 36.7159 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 : 0.969 ------------------------------------------------------------------------------- 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 7602 Z= 0.258 Angle : 0.682 8.202 10265 Z= 0.354 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 *********************** 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 : 0.979 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: 0.2370 time to fit residues: 46.1946 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 : 0.957 ------------------------------------------------------------------------------- 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 7602 Z= 0.384 Angle : 0.690 6.460 10265 Z= 0.364 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 *********************** 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 : 0.859 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: 0.2333 time to fit residues: 44.4326 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 : 0.937 ------------------------------------------------------------------------------- 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: 6.9990 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: 2.9788 ------------------------------------------------------------------------------- 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** ** 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 = 0.3592 r_free = 0.3592 target = 0.070599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049392 restraints weight = 32783.044| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 6.66 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7602 Z= 0.255 Angle : 0.619 7.936 10265 Z= 0.323 Chirality : 0.044 0.141 1207 Planarity : 0.003 0.031 1316 Dihedral : 4.563 18.150 1022 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.43 % Allowed : 24.79 % 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: -0.81 (0.27), residues: 959 helix: 0.76 (0.32), residues: 261 sheet: -0.44 (0.29), residues: 332 loop : -1.50 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 *********************** 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 171 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 0.956 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: 0.9191 (pptt) cc_final: 0.8960 (pptt) REVERT: E 469 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9199 (mp) REVERT: E 487 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8428 (m) REVERT: E 498 ASP cc_start: 0.9230 (p0) cc_final: 0.8931 (p0) REVERT: E 542 ARG cc_start: 0.9080 (ttm-80) cc_final: 0.8874 (ttm170) REVERT: B 1 MET cc_start: 0.9166 (ppp) cc_final: 0.8324 (ppp) REVERT: B 20 LYS cc_start: 0.9549 (tttt) cc_final: 0.9286 (tttp) REVERT: B 68 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7722 (pmm) REVERT: B 135 CYS cc_start: 0.8236 (t) cc_final: 0.7824 (m) REVERT: B 139 MET cc_start: 0.9415 (ttp) cc_final: 0.8970 (tmm) REVERT: B 244 MET cc_start: 0.9098 (tpp) cc_final: 0.8810 (tpt) REVERT: C 12 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8689 (tt) REVERT: C 28 TRP cc_start: 0.8341 (m100) cc_final: 0.7834 (m-90) REVERT: C 44 HIS cc_start: 0.9252 (OUTLIER) cc_final: 0.9003 (t-90) REVERT: C 249 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: D 112 SER cc_start: 0.7851 (OUTLIER) cc_final: 0.7572 (p) outliers start: 46 outliers final: 24 residues processed: 159 average time/residue: 0.2309 time to fit residues: 47.6784 Evaluate side-chains 138 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 455 PHE 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 553 SER 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 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 C residue 249 TYR 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 261 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.070229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048903 restraints weight = 32524.460| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 6.67 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7602 Z= 0.284 Angle : 0.652 11.058 10265 Z= 0.335 Chirality : 0.044 0.175 1207 Planarity : 0.003 0.031 1316 Dihedral : 4.579 19.724 1022 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.90 % Allowed : 25.97 % 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: -0.73 (0.27), residues: 959 helix: 0.86 (0.32), residues: 257 sheet: -0.38 (0.29), residues: 328 loop : -1.46 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 28 HIS 0.005 0.001 HIS C 44 PHE 0.023 0.002 PHE B 215 TYR 0.037 0.002 TYR E 408 ARG 0.006 0.001 ARG C 149 *********************** 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 162 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.995 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: 0.9190 (pptt) cc_final: 0.8969 (pptt) REVERT: E 469 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9200 (mp) REVERT: E 487 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8430 (m) REVERT: E 498 ASP cc_start: 0.9249 (p0) cc_final: 0.8925 (p0) REVERT: E 500 PHE cc_start: 0.9296 (m-80) cc_final: 0.9047 (m-80) REVERT: E 542 ARG cc_start: 0.9075 (ttm-80) cc_final: 0.8834 (ttm170) REVERT: B 1 MET cc_start: 0.9150 (ppp) cc_final: 0.8371 (ppp) REVERT: B 20 LYS cc_start: 0.9565 (tttt) cc_final: 0.9155 (mtpp) REVERT: B 40 MET cc_start: 0.7771 (tmm) cc_final: 0.7447 (tmm) REVERT: B 68 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7537 (pmm) REVERT: B 135 CYS cc_start: 0.8335 (t) cc_final: 0.7818 (m) REVERT: B 199 MET cc_start: 0.6627 (ttp) cc_final: 0.6233 (ttp) REVERT: B 244 MET cc_start: 0.9044 (tpp) cc_final: 0.8711 (tpt) REVERT: C 12 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8756 (tt) REVERT: C 28 TRP cc_start: 0.8335 (m100) cc_final: 0.7842 (m-90) REVERT: C 44 HIS cc_start: 0.9217 (OUTLIER) cc_final: 0.8936 (t-90) REVERT: C 61 ARG cc_start: 0.9092 (mtp85) cc_final: 0.8776 (mtp85) REVERT: C 249 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: D 17 GLU cc_start: 0.9536 (OUTLIER) cc_final: 0.9306 (mp0) REVERT: D 61 ARG cc_start: 0.7602 (tmm-80) cc_final: 0.7140 (ttp80) REVERT: D 112 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7584 (p) REVERT: D 249 TYR cc_start: 0.8296 (m-80) cc_final: 0.7968 (m-10) outliers start: 50 outliers final: 36 residues processed: 151 average time/residue: 0.2343 time to fit residues: 45.9802 Evaluate side-chains 149 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 455 PHE 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 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 224 THR Chi-restraints excluded: chain B residue 235 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 17 GLU Chi-restraints excluded: chain D residue 87 ILE 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: 10.0000 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.071589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050412 restraints weight = 32648.349| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 6.80 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7602 Z= 0.180 Angle : 0.614 9.540 10265 Z= 0.311 Chirality : 0.044 0.145 1207 Planarity : 0.003 0.030 1316 Dihedral : 4.313 16.160 1022 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.08 % Allowed : 25.97 % Favored : 68.95 % 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: 1.02 (0.33), residues: 259 sheet: -0.32 (0.29), residues: 328 loop : -1.40 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 28 HIS 0.004 0.001 HIS C 44 PHE 0.019 0.001 PHE D 207 TYR 0.038 0.002 TYR E 408 ARG 0.007 0.001 ARG C 149 *********************** 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 164 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 469 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9164 (mp) REVERT: E 487 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8341 (m) REVERT: E 498 ASP cc_start: 0.9249 (p0) cc_final: 0.8916 (p0) REVERT: E 500 PHE cc_start: 0.9241 (m-80) cc_final: 0.8997 (m-80) REVERT: E 542 ARG cc_start: 0.8987 (ttm-80) cc_final: 0.8727 (ttm170) REVERT: B 1 MET cc_start: 0.9142 (ppp) cc_final: 0.8792 (ppp) REVERT: B 40 MET cc_start: 0.7743 (tmm) cc_final: 0.7413 (tmm) REVERT: B 68 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7512 (pmm) REVERT: B 135 CYS cc_start: 0.8333 (t) cc_final: 0.7956 (m) REVERT: B 139 MET cc_start: 0.9385 (ttp) cc_final: 0.8970 (tmm) REVERT: B 244 MET cc_start: 0.9065 (tpp) cc_final: 0.8747 (tpt) REVERT: C 12 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8732 (tt) REVERT: C 28 TRP cc_start: 0.8300 (m100) cc_final: 0.7694 (m-90) REVERT: C 44 HIS cc_start: 0.9244 (OUTLIER) cc_final: 0.8887 (t70) REVERT: C 61 ARG cc_start: 0.9147 (mtp85) cc_final: 0.8911 (mtp85) REVERT: C 149 ARG cc_start: 0.8478 (ttp-110) cc_final: 0.8182 (ptm-80) REVERT: D 61 ARG cc_start: 0.7498 (tmm-80) cc_final: 0.7261 (ttp80) REVERT: D 64 ARG cc_start: 0.9506 (tmt170) cc_final: 0.9229 (tmm-80) REVERT: D 211 TYR cc_start: 0.8701 (m-10) cc_final: 0.8474 (m-10) REVERT: D 249 TYR cc_start: 0.8214 (m-80) cc_final: 0.7956 (m-10) outliers start: 43 outliers final: 27 residues processed: 155 average time/residue: 0.2349 time to fit residues: 46.8900 Evaluate side-chains 145 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 514 LYS Chi-restraints excluded: chain E residue 519 ILE Chi-restraints excluded: chain E residue 550 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 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 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 185 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.0010 chunk 72 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.071844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.050670 restraints weight = 32053.482| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 6.69 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7602 Z= 0.186 Angle : 0.630 9.780 10265 Z= 0.320 Chirality : 0.044 0.178 1207 Planarity : 0.003 0.029 1316 Dihedral : 4.306 15.923 1022 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.08 % Allowed : 27.15 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 260 sheet: -0.20 (0.30), residues: 322 loop : -1.44 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 28 HIS 0.006 0.001 HIS E 507 PHE 0.015 0.002 PHE D 207 TYR 0.037 0.002 TYR E 408 ARG 0.006 0.001 ARG C 149 *********************** 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: 43 poor density : 116 time to evaluate : 0.868 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: 0.9419 (OUTLIER) cc_final: 0.9189 (mp) REVERT: E 498 ASP cc_start: 0.9257 (p0) cc_final: 0.9005 (p0) REVERT: E 533 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8208 (pp30) REVERT: E 542 ARG cc_start: 0.9003 (ttm-80) cc_final: 0.8704 (ttm170) REVERT: B 1 MET cc_start: 0.9152 (ppp) cc_final: 0.8807 (ppp) REVERT: B 40 MET cc_start: 0.7783 (tmm) cc_final: 0.7448 (tmm) REVERT: B 135 CYS cc_start: 0.8387 (t) cc_final: 0.8057 (m) REVERT: B 199 MET cc_start: 0.7010 (tmm) cc_final: 0.6768 (tmm) REVERT: B 244 MET cc_start: 0.9032 (tpp) cc_final: 0.8719 (tpt) REVERT: C 12 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8760 (tt) REVERT: C 28 TRP cc_start: 0.8345 (m100) cc_final: 0.7659 (m-90) REVERT: C 44 HIS cc_start: 0.9335 (OUTLIER) cc_final: 0.9111 (t-90) REVERT: C 149 ARG cc_start: 0.8469 (ttp-110) cc_final: 0.8163 (ptm-80) REVERT: D 40 MET cc_start: 0.8654 (tmm) cc_final: 0.8384 (tmm) REVERT: D 61 ARG cc_start: 0.7652 (tmm-80) cc_final: 0.7403 (ttp80) REVERT: D 249 TYR cc_start: 0.8259 (m-80) cc_final: 0.8028 (m-10) outliers start: 43 outliers final: 31 residues processed: 150 average time/residue: 0.2186 time to fit residues: 42.6691 Evaluate side-chains 144 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 12 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 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 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 158 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 261 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 0.0470 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3613 r_free = 0.3613 target = 0.071349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050052 restraints weight = 32769.954| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 6.73 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7602 Z= 0.217 Angle : 0.645 11.063 10265 Z= 0.327 Chirality : 0.045 0.239 1207 Planarity : 0.003 0.033 1316 Dihedral : 4.319 17.029 1022 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.31 % Allowed : 26.92 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.32), residues: 260 sheet: -0.20 (0.30), residues: 324 loop : -1.38 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 28 HIS 0.005 0.001 HIS C 44 PHE 0.021 0.002 PHE D 207 TYR 0.040 0.002 TYR E 408 ARG 0.006 0.001 ARG B 146 *********************** 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 156 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.891 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 469 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9196 (mp) REVERT: E 498 ASP cc_start: 0.9287 (p0) cc_final: 0.8852 (p0) REVERT: E 500 PHE cc_start: 0.9337 (m-80) cc_final: 0.9061 (m-80) REVERT: E 533 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8298 (pp30) REVERT: E 542 ARG cc_start: 0.8940 (ttm-80) cc_final: 0.8638 (ttm170) REVERT: B 1 MET cc_start: 0.9140 (ppp) cc_final: 0.8824 (ppp) REVERT: B 20 LYS cc_start: 0.9584 (tttt) cc_final: 0.9316 (tttp) REVERT: B 40 MET cc_start: 0.7810 (tmm) cc_final: 0.7490 (tmm) REVERT: B 66 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9091 (tp) REVERT: B 135 CYS cc_start: 0.8408 (t) cc_final: 0.8114 (m) REVERT: B 199 MET cc_start: 0.7094 (tmm) cc_final: 0.6859 (tmm) REVERT: B 244 MET cc_start: 0.9041 (tpp) cc_final: 0.8718 (tpt) REVERT: C 12 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8743 (tt) REVERT: C 44 HIS cc_start: 0.9305 (OUTLIER) cc_final: 0.8959 (t70) REVERT: C 149 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.8177 (ttp80) REVERT: D 112 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7619 (p) REVERT: D 249 TYR cc_start: 0.8323 (m-80) cc_final: 0.8095 (m-10) outliers start: 45 outliers final: 34 residues processed: 147 average time/residue: 0.2234 time to fit residues: 43.0799 Evaluate side-chains 148 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 455 PHE Chi-restraints excluded: chain E residue 469 LEU 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 12 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 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 255 ILE 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 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: 2.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 40.0000 chunk 69 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.072012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050577 restraints weight = 33017.263| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 6.89 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7602 Z= 0.194 Angle : 0.654 10.672 10265 Z= 0.329 Chirality : 0.045 0.199 1207 Planarity : 0.003 0.029 1316 Dihedral : 4.286 16.129 1022 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.08 % Allowed : 27.15 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.27), residues: 959 helix: 0.75 (0.33), residues: 259 sheet: -0.20 (0.30), residues: 320 loop : -1.33 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 28 HIS 0.006 0.001 HIS C 44 PHE 0.039 0.002 PHE E 407 TYR 0.038 0.002 TYR E 408 ARG 0.009 0.001 ARG D 64 *********************** 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 156 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 113 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 469 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9184 (mp) REVERT: E 487 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8535 (m) REVERT: E 498 ASP cc_start: 0.9277 (p0) cc_final: 0.8851 (p0) REVERT: E 500 PHE cc_start: 0.9334 (m-80) cc_final: 0.9047 (m-80) REVERT: E 533 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8242 (pp30) REVERT: E 542 ARG cc_start: 0.8937 (ttm-80) cc_final: 0.8657 (ttm170) REVERT: B 1 MET cc_start: 0.9158 (ppp) cc_final: 0.8833 (ppp) REVERT: B 20 LYS cc_start: 0.9594 (tttt) cc_final: 0.9311 (tttp) REVERT: B 40 MET cc_start: 0.7850 (tmm) cc_final: 0.7494 (tmm) REVERT: B 66 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9089 (tp) REVERT: B 135 CYS cc_start: 0.8356 (t) cc_final: 0.8106 (m) REVERT: B 199 MET cc_start: 0.7147 (tmm) cc_final: 0.6919 (tmm) REVERT: B 244 MET cc_start: 0.9017 (tpp) cc_final: 0.8695 (tpt) REVERT: C 12 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8744 (tt) REVERT: C 44 HIS cc_start: 0.9320 (OUTLIER) cc_final: 0.8922 (t-170) REVERT: D 112 SER cc_start: 0.7943 (OUTLIER) cc_final: 0.7695 (p) REVERT: D 249 TYR cc_start: 0.8295 (m-80) cc_final: 0.8087 (m-10) outliers start: 43 outliers final: 34 residues processed: 146 average time/residue: 0.2083 time to fit residues: 40.4696 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 : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 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 533 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 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 255 ILE 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 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: 3.9990 chunk 79 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 0.0570 chunk 11 optimal weight: 0.0970 chunk 87 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.071766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050379 restraints weight = 33172.236| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 6.86 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7602 Z= 0.219 Angle : 0.676 10.758 10265 Z= 0.342 Chirality : 0.045 0.187 1207 Planarity : 0.003 0.037 1316 Dihedral : 4.367 22.526 1022 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.96 % Allowed : 27.74 % Favored : 67.30 % 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: -0.70 (0.27), residues: 959 helix: 0.64 (0.33), residues: 259 sheet: -0.26 (0.30), residues: 322 loop : -1.34 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 28 HIS 0.006 0.001 HIS C 44 PHE 0.019 0.002 PHE D 207 TYR 0.039 0.002 TYR E 408 ARG 0.009 0.001 ARG C 149 ********************** 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 155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.951 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 469 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9186 (mp) REVERT: E 487 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8493 (m) REVERT: E 498 ASP cc_start: 0.9286 (p0) cc_final: 0.8857 (p0) REVERT: E 500 PHE cc_start: 0.9347 (m-80) cc_final: 0.9080 (m-80) REVERT: B 1 MET cc_start: 0.9155 (ppp) cc_final: 0.8840 (ppp) REVERT: B 40 MET cc_start: 0.7856 (tmm) cc_final: 0.7518 (tmm) REVERT: B 66 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9073 (tp) REVERT: B 135 CYS cc_start: 0.8381 (t) cc_final: 0.8154 (m) REVERT: B 199 MET cc_start: 0.7195 (tmm) cc_final: 0.6977 (tmm) REVERT: B 244 MET cc_start: 0.9043 (tpp) cc_final: 0.8714 (tpt) REVERT: C 12 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8764 (tt) REVERT: C 44 HIS cc_start: 0.9290 (OUTLIER) cc_final: 0.8958 (t70) REVERT: C 149 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.8240 (ptm-80) REVERT: D 112 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7720 (p) REVERT: D 229 MET cc_start: 0.9114 (pmm) cc_final: 0.8808 (pmm) REVERT: D 249 TYR cc_start: 0.8314 (m-80) cc_final: 0.8093 (m-10) outliers start: 42 outliers final: 34 residues processed: 146 average time/residue: 0.2140 time to fit residues: 41.2325 Evaluate side-chains 147 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 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 66 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 CYS Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 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 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 255 ILE Chi-restraints excluded: chain D residue 2 PHE 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 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: 0.5980 chunk 50 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 30 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.072192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.050917 restraints weight = 32470.011| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 6.83 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7602 Z= 0.200 Angle : 0.673 9.632 10265 Z= 0.340 Chirality : 0.045 0.177 1207 Planarity : 0.003 0.037 1316 Dihedral : 4.323 21.768 1022 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.60 % Allowed : 27.27 % 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: -0.74 (0.27), residues: 959 helix: 0.56 (0.32), residues: 259 sheet: -0.27 (0.30), residues: 322 loop : -1.35 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 28 HIS 0.005 0.001 HIS C 44 PHE 0.015 0.002 PHE E 407 TYR 0.039 0.002 TYR E 408 ARG 0.009 0.001 ARG C 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3740.31 seconds wall clock time: 65 minutes 7.41 seconds (3907.41 seconds total)