Starting phenix.real_space_refine on Wed Sep 17 22:54:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lic_23372/09_2025/7lic_23372.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lic_23372/09_2025/7lic_23372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lic_23372/09_2025/7lic_23372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lic_23372/09_2025/7lic_23372.map" model { file = "/net/cci-nas-00/data/ceres_data/7lic_23372/09_2025/7lic_23372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lic_23372/09_2025/7lic_23372.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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 120 5.16 5 C 7888 2.51 5 N 1920 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11980 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2995 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 9, 'TRANS': 367} Chain breaks: 3 Restraints were copied for chains: B, C, D Time building chain proxies: 2.13, per 1000 atoms: 0.18 Number of scatterers: 11980 At special positions: 0 Unit cell: (111.24, 110.21, 89.61, 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 120 16.00 O 2052 8.00 N 1920 7.00 C 7888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 570.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 removed outlier: 3.633A pdb=" N HIS A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 removed outlier: 3.760A pdb=" N LYS A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 48 through 75 Processing helix chain 'A' and resid 78 through 105 removed outlier: 3.646A pdb=" N LEU A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.851A pdb=" N GLU A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 167 removed outlier: 3.816A pdb=" N SER A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.606A pdb=" N LEU A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 247 removed outlier: 3.767A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 318 through 366 removed outlier: 3.841A pdb=" N SER A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 407 removed outlier: 4.265A pdb=" N GLY A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.682A pdb=" N GLN A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 468 Processing helix chain 'B' and resid 13 through 31 Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.760A pdb=" N LYS B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 48 through 75 Processing helix chain 'B' and resid 78 through 105 removed outlier: 3.645A pdb=" N LEU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 118 removed outlier: 3.852A pdb=" N GLU B 118 " --> pdb=" O ASN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 167 removed outlier: 3.816A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Proline residue: B 162 - end of helix removed outlier: 3.605A pdb=" N LEU B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 247 removed outlier: 3.765A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 318 through 366 removed outlier: 3.841A pdb=" N SER B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 407 removed outlier: 4.265A pdb=" N GLY B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 387 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 418 through 433 removed outlier: 3.683A pdb=" N GLN B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 468 Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 44 through 47 removed outlier: 3.761A pdb=" N LYS C 47 " --> pdb=" O ASN C 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 44 through 47' Processing helix chain 'C' and resid 48 through 75 Processing helix chain 'C' and resid 78 through 105 removed outlier: 3.645A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 118 removed outlier: 3.851A pdb=" N GLU C 118 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 167 removed outlier: 3.815A pdb=" N SER C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) Proline residue: C 162 - end of helix removed outlier: 3.606A pdb=" N LEU C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 247 removed outlier: 3.767A pdb=" N GLU C 199 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 318 through 366 removed outlier: 3.841A pdb=" N SER C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 407 removed outlier: 4.265A pdb=" N GLY C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 387 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 418 through 433 removed outlier: 3.683A pdb=" N GLN C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 468 Processing helix chain 'D' and resid 13 through 31 Processing helix chain 'D' and resid 44 through 47 removed outlier: 3.761A pdb=" N LYS D 47 " --> pdb=" O ASN D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 44 through 47' Processing helix chain 'D' and resid 48 through 75 Processing helix chain 'D' and resid 78 through 105 removed outlier: 3.646A pdb=" N LEU D 83 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 removed outlier: 3.851A pdb=" N GLU D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 167 removed outlier: 3.816A pdb=" N SER D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) Proline residue: D 162 - end of helix removed outlier: 3.605A pdb=" N LEU D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 247 removed outlier: 3.767A pdb=" N GLU D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 318 through 366 removed outlier: 3.840A pdb=" N SER D 343 " --> pdb=" O GLN D 339 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA D 366 " --> pdb=" O TYR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 407 removed outlier: 4.264A pdb=" N GLY D 376 " --> pdb=" O THR D 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 387 " --> pdb=" O TYR D 383 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 418 through 433 removed outlier: 3.683A pdb=" N GLN D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 468 972 hydrogen bonds defined for protein. 2892 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: 1.86 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3558 1.34 - 1.46: 2825 1.46 - 1.58: 5697 1.58 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 12252 Sorted by residual: bond pdb=" C SER D 195 " pdb=" N PRO D 196 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.20e-02 6.94e+03 7.07e+00 bond pdb=" C SER C 195 " pdb=" N PRO C 196 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.20e-02 6.94e+03 6.96e+00 bond pdb=" C SER A 195 " pdb=" N PRO A 196 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.20e-02 6.94e+03 6.80e+00 bond pdb=" C SER B 195 " pdb=" N PRO B 196 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.20e-02 6.94e+03 6.67e+00 bond pdb=" C VAL D 374 " pdb=" N PRO D 375 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.51e-02 4.39e+03 2.13e+00 ... (remaining 12247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 15678 1.58 - 3.16: 758 3.16 - 4.73: 144 4.73 - 6.31: 24 6.31 - 7.89: 8 Bond angle restraints: 16612 Sorted by residual: angle pdb=" CA THR C 367 " pdb=" C THR C 367 " pdb=" N SER C 368 " ideal model delta sigma weight residual 115.55 120.52 -4.97 1.33e+00 5.65e-01 1.40e+01 angle pdb=" CA THR A 367 " pdb=" C THR A 367 " pdb=" N SER A 368 " ideal model delta sigma weight residual 115.55 120.51 -4.96 1.33e+00 5.65e-01 1.39e+01 angle pdb=" C THR A 367 " pdb=" CA THR A 367 " pdb=" CB THR A 367 " ideal model delta sigma weight residual 109.50 115.79 -6.29 1.69e+00 3.50e-01 1.39e+01 angle pdb=" CA THR B 367 " pdb=" C THR B 367 " pdb=" N SER B 368 " ideal model delta sigma weight residual 115.55 120.50 -4.95 1.33e+00 5.65e-01 1.39e+01 angle pdb=" C THR C 367 " pdb=" CA THR C 367 " pdb=" CB THR C 367 " ideal model delta sigma weight residual 109.50 115.75 -6.25 1.69e+00 3.50e-01 1.37e+01 ... (remaining 16607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 6414 17.55 - 35.10: 598 35.10 - 52.65: 152 52.65 - 70.20: 24 70.20 - 87.75: 8 Dihedral angle restraints: 7196 sinusoidal: 2740 harmonic: 4456 Sorted by residual: dihedral pdb=" CA ASN A 85 " pdb=" C ASN A 85 " pdb=" N ILE A 86 " pdb=" CA ILE A 86 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASN C 85 " pdb=" C ASN C 85 " pdb=" N ILE C 86 " pdb=" CA ILE C 86 " ideal model delta harmonic sigma weight residual -180.00 -159.18 -20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN D 85 " pdb=" C ASN D 85 " pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 7193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1275 0.037 - 0.074: 522 0.074 - 0.111: 151 0.111 - 0.148: 32 0.148 - 0.185: 12 Chirality restraints: 1992 Sorted by residual: chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CG LEU B 83 " pdb=" CB LEU B 83 " pdb=" CD1 LEU B 83 " pdb=" CD2 LEU B 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CG LEU A 83 " pdb=" CB LEU A 83 " pdb=" CD1 LEU A 83 " pdb=" CD2 LEU A 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1989 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 96 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C CYS B 96 " 0.046 2.00e-02 2.50e+03 pdb=" O CYS B 96 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 97 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 96 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C CYS A 96 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS A 96 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 97 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 96 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C CYS C 96 " -0.045 2.00e-02 2.50e+03 pdb=" O CYS C 96 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL C 97 " 0.015 2.00e-02 2.50e+03 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3052 2.79 - 3.32: 12148 3.32 - 3.84: 19802 3.84 - 4.37: 21248 4.37 - 4.90: 37126 Nonbonded interactions: 93376 Sorted by model distance: nonbonded pdb=" OE1 GLU C 397 " pdb=" NH1 ARG D 442 " model vdw 2.261 3.120 nonbonded pdb=" OG SER A 78 " pdb=" OE1 GLN A 81 " model vdw 2.281 3.040 nonbonded pdb=" OG SER D 78 " pdb=" OE1 GLN D 81 " model vdw 2.281 3.040 nonbonded pdb=" OG SER B 78 " pdb=" OE1 GLN B 81 " model vdw 2.281 3.040 nonbonded pdb=" OG SER C 78 " pdb=" OE1 GLN C 81 " model vdw 2.282 3.040 ... (remaining 93371 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 0.033 12252 Z= 0.219 Angle : 0.808 7.888 16612 Z= 0.482 Chirality : 0.045 0.185 1992 Planarity : 0.007 0.057 1988 Dihedral : 15.151 87.752 4300 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.90 % Allowed : 5.00 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.20), residues: 1476 helix: -0.08 (0.14), residues: 1188 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 422 TYR 0.017 0.002 TYR D 204 PHE 0.011 0.001 PHE D 450 TRP 0.018 0.002 TRP D 155 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00394 (12252) covalent geometry : angle 0.80812 (16612) hydrogen bonds : bond 0.13588 ( 972) hydrogen bonds : angle 5.13909 ( 2892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 406 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8279 (t0) cc_final: 0.7652 (t0) REVERT: A 110 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7839 (tp30) REVERT: A 128 TYR cc_start: 0.8299 (t80) cc_final: 0.8029 (t80) REVERT: A 158 TRP cc_start: 0.7992 (t-100) cc_final: 0.7602 (m-10) REVERT: A 205 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 214 THR cc_start: 0.8884 (p) cc_final: 0.8682 (m) REVERT: A 419 ASP cc_start: 0.7632 (p0) cc_final: 0.7397 (p0) REVERT: B 54 TYR cc_start: 0.8497 (t80) cc_final: 0.8273 (t80) REVERT: B 84 ASN cc_start: 0.8203 (t0) cc_final: 0.7849 (t0) REVERT: B 110 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7930 (tp30) REVERT: B 128 TYR cc_start: 0.8213 (t80) cc_final: 0.7962 (t80) REVERT: B 158 TRP cc_start: 0.8032 (t-100) cc_final: 0.7764 (m-10) REVERT: B 198 ASN cc_start: 0.7890 (t0) cc_final: 0.7617 (t0) REVERT: B 205 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 397 GLU cc_start: 0.7850 (tp30) cc_final: 0.7641 (tp30) REVERT: B 419 ASP cc_start: 0.7689 (p0) cc_final: 0.7422 (p0) REVERT: C 45 GLN cc_start: 0.7268 (pm20) cc_final: 0.6914 (pm20) REVERT: C 54 TYR cc_start: 0.8194 (t80) cc_final: 0.7895 (t80) REVERT: C 84 ASN cc_start: 0.8204 (t0) cc_final: 0.7682 (t0) REVERT: C 128 TYR cc_start: 0.8203 (t80) cc_final: 0.7939 (t80) REVERT: C 158 TRP cc_start: 0.8054 (t-100) cc_final: 0.7668 (m-10) REVERT: C 184 VAL cc_start: 0.7336 (p) cc_final: 0.6906 (p) REVERT: C 198 ASN cc_start: 0.7887 (t0) cc_final: 0.7342 (t0) REVERT: C 205 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 214 THR cc_start: 0.9045 (p) cc_final: 0.8786 (p) REVERT: C 351 PHE cc_start: 0.8671 (t80) cc_final: 0.8414 (m-80) REVERT: C 419 ASP cc_start: 0.7718 (p0) cc_final: 0.7486 (p0) REVERT: D 84 ASN cc_start: 0.8322 (t0) cc_final: 0.7644 (t0) REVERT: D 110 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7888 (tp30) REVERT: D 128 TYR cc_start: 0.8325 (t80) cc_final: 0.7980 (t80) REVERT: D 158 TRP cc_start: 0.7974 (t-100) cc_final: 0.7643 (m-10) REVERT: D 205 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7998 (tm-30) outliers start: 12 outliers final: 4 residues processed: 418 average time/residue: 0.1013 time to fit residues: 61.9946 Evaluate side-chains 233 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 229 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS B 433 GLN C 33 HIS C 420 HIS C 433 GLN D 233 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.099062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079919 restraints weight = 32567.799| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.54 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12252 Z= 0.178 Angle : 0.650 7.128 16612 Z= 0.340 Chirality : 0.038 0.138 1992 Planarity : 0.005 0.047 1988 Dihedral : 3.969 14.440 1628 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.39 % Allowed : 16.34 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.22), residues: 1476 helix: 1.77 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.60 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 43 TYR 0.021 0.002 TYR C 204 PHE 0.013 0.001 PHE C 450 TRP 0.019 0.002 TRP D 155 HIS 0.004 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00386 (12252) covalent geometry : angle 0.64984 (16612) hydrogen bonds : bond 0.05910 ( 972) hydrogen bonds : angle 3.85804 ( 2892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8919 (t0) cc_final: 0.8696 (t0) REVERT: A 93 LEU cc_start: 0.9060 (tp) cc_final: 0.8849 (tp) REVERT: A 110 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8423 (tp30) REVERT: A 158 TRP cc_start: 0.8473 (t-100) cc_final: 0.7470 (m-10) REVERT: A 197 MET cc_start: 0.6381 (tpp) cc_final: 0.6152 (tpp) REVERT: A 205 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 214 THR cc_start: 0.8499 (p) cc_final: 0.8270 (t) REVERT: A 233 HIS cc_start: 0.8841 (t-90) cc_final: 0.8496 (t70) REVERT: A 377 MET cc_start: 0.8667 (mpp) cc_final: 0.8183 (mpp) REVERT: A 394 LEU cc_start: 0.9334 (mt) cc_final: 0.9132 (mt) REVERT: A 419 ASP cc_start: 0.8780 (p0) cc_final: 0.8547 (p0) REVERT: B 84 ASN cc_start: 0.8877 (t0) cc_final: 0.8558 (t0) REVERT: B 110 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8437 (tp30) REVERT: B 157 MET cc_start: 0.8558 (tpt) cc_final: 0.8277 (ttm) REVERT: B 158 TRP cc_start: 0.8401 (t-100) cc_final: 0.7483 (m-10) REVERT: B 205 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 222 MET cc_start: 0.8703 (tmm) cc_final: 0.8369 (tmm) REVERT: B 233 HIS cc_start: 0.8840 (t70) cc_final: 0.8503 (t70) REVERT: C 17 LEU cc_start: 0.9321 (tt) cc_final: 0.9100 (pp) REVERT: C 54 TYR cc_start: 0.8072 (t80) cc_final: 0.7781 (t80) REVERT: C 84 ASN cc_start: 0.8927 (t0) cc_final: 0.8705 (t0) REVERT: C 110 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8605 (tp30) REVERT: C 128 TYR cc_start: 0.8784 (t80) cc_final: 0.8232 (t80) REVERT: C 198 ASN cc_start: 0.8111 (t0) cc_final: 0.7609 (t0) REVERT: C 205 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 214 THR cc_start: 0.8607 (p) cc_final: 0.8245 (t) REVERT: C 222 MET cc_start: 0.8739 (tmm) cc_final: 0.8380 (tmm) REVERT: C 239 MET cc_start: 0.8874 (tpp) cc_final: 0.8476 (tpp) REVERT: C 342 TYR cc_start: 0.7506 (m-80) cc_final: 0.7121 (m-10) REVERT: C 419 ASP cc_start: 0.8842 (p0) cc_final: 0.8634 (p0) REVERT: D 20 TRP cc_start: 0.8851 (t-100) cc_final: 0.8574 (t-100) REVERT: D 84 ASN cc_start: 0.8815 (t0) cc_final: 0.8537 (t0) REVERT: D 110 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8310 (tp30) REVERT: D 158 TRP cc_start: 0.8404 (t-100) cc_final: 0.7502 (m-10) REVERT: D 205 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8028 (tm-30) REVERT: D 214 THR cc_start: 0.8654 (m) cc_final: 0.8358 (t) REVERT: D 377 MET cc_start: 0.8712 (mpp) cc_final: 0.8336 (mpp) outliers start: 32 outliers final: 16 residues processed: 292 average time/residue: 0.0796 time to fit residues: 36.5844 Evaluate side-chains 244 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS B 198 ASN B 407 HIS ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.106702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.088298 restraints weight = 30326.891| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 4.41 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12252 Z= 0.139 Angle : 0.592 7.462 16612 Z= 0.305 Chirality : 0.038 0.135 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.725 15.527 1624 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.91 % Allowed : 18.96 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.22), residues: 1476 helix: 2.33 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 431 TYR 0.020 0.002 TYR B 99 PHE 0.009 0.001 PHE C 183 TRP 0.022 0.002 TRP B 20 HIS 0.017 0.001 HIS C 420 Details of bonding type rmsd covalent geometry : bond 0.00291 (12252) covalent geometry : angle 0.59227 (16612) hydrogen bonds : bond 0.05125 ( 972) hydrogen bonds : angle 3.60424 ( 2892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8765 (m110) cc_final: 0.8551 (m-40) REVERT: A 110 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8249 (tp30) REVERT: A 205 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 214 THR cc_start: 0.8449 (p) cc_final: 0.8182 (t) REVERT: A 239 MET cc_start: 0.8761 (tpp) cc_final: 0.8425 (tpp) REVERT: A 352 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8532 (t) REVERT: A 377 MET cc_start: 0.8591 (mpp) cc_final: 0.8229 (mpp) REVERT: A 394 LEU cc_start: 0.9226 (mt) cc_final: 0.9009 (mt) REVERT: A 419 ASP cc_start: 0.8703 (p0) cc_final: 0.8480 (p0) REVERT: B 84 ASN cc_start: 0.8835 (t0) cc_final: 0.8533 (t0) REVERT: B 110 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8484 (tp30) REVERT: B 141 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8302 (pttp) REVERT: B 157 MET cc_start: 0.8470 (tpt) cc_final: 0.8151 (ttm) REVERT: B 158 TRP cc_start: 0.8155 (t-100) cc_final: 0.7509 (m-10) REVERT: B 197 MET cc_start: 0.6319 (tpp) cc_final: 0.6085 (tpp) REVERT: B 205 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8136 (tm-30) REVERT: B 214 THR cc_start: 0.8659 (m) cc_final: 0.8353 (t) REVERT: B 222 MET cc_start: 0.8710 (tmm) cc_final: 0.8482 (tmm) REVERT: B 342 TYR cc_start: 0.7434 (m-80) cc_final: 0.6662 (m-10) REVERT: B 352 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8408 (t) REVERT: B 377 MET cc_start: 0.8844 (mmm) cc_final: 0.8391 (mpp) REVERT: B 379 LEU cc_start: 0.7785 (tp) cc_final: 0.7445 (tp) REVERT: C 29 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8571 (mpp80) REVERT: C 54 TYR cc_start: 0.8109 (t80) cc_final: 0.7867 (t80) REVERT: C 110 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8880 (tm-30) REVERT: C 128 TYR cc_start: 0.8806 (t80) cc_final: 0.8363 (t80) REVERT: C 205 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 212 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8971 (mt) REVERT: C 214 THR cc_start: 0.8623 (p) cc_final: 0.8275 (t) REVERT: C 222 MET cc_start: 0.8720 (tmm) cc_final: 0.8460 (tmm) REVERT: C 239 MET cc_start: 0.8899 (tpp) cc_final: 0.6877 (tpp) REVERT: C 242 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7819 (pp20) REVERT: C 342 TYR cc_start: 0.7365 (m-80) cc_final: 0.6948 (m-10) REVERT: C 352 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8629 (t) REVERT: C 377 MET cc_start: 0.8462 (mmt) cc_final: 0.8245 (mmt) REVERT: C 419 ASP cc_start: 0.8639 (p0) cc_final: 0.8433 (p0) REVERT: D 84 ASN cc_start: 0.8774 (t0) cc_final: 0.8537 (t0) REVERT: D 110 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8305 (tp30) REVERT: D 157 MET cc_start: 0.8315 (tpt) cc_final: 0.7956 (ttm) REVERT: D 158 TRP cc_start: 0.8320 (t-100) cc_final: 0.7525 (m-10) REVERT: D 197 MET cc_start: 0.6026 (tpp) cc_final: 0.5748 (tpp) REVERT: D 205 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8027 (tm-30) REVERT: D 214 THR cc_start: 0.8636 (m) cc_final: 0.8352 (t) REVERT: D 352 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8575 (t) REVERT: D 377 MET cc_start: 0.8611 (mpp) cc_final: 0.8274 (mpp) outliers start: 39 outliers final: 21 residues processed: 295 average time/residue: 0.0806 time to fit residues: 37.5484 Evaluate side-chains 261 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 415 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 120 optimal weight: 4.9990 chunk 124 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.0040 chunk 113 optimal weight: 2.9990 overall best weight: 0.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 HIS B 233 HIS ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.103058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084189 restraints weight = 31923.337| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.43 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12252 Z= 0.130 Angle : 0.568 6.025 16612 Z= 0.294 Chirality : 0.038 0.174 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.543 14.973 1624 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.99 % Allowed : 20.60 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.22), residues: 1476 helix: 2.54 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.23 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.023 0.001 TYR B 99 PHE 0.007 0.001 PHE A 450 TRP 0.018 0.002 TRP A 20 HIS 0.004 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00276 (12252) covalent geometry : angle 0.56799 (16612) hydrogen bonds : bond 0.04663 ( 972) hydrogen bonds : angle 3.45483 ( 2892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 20 TRP cc_start: 0.8735 (t-100) cc_final: 0.8508 (t-100) REVERT: A 110 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8338 (tp30) REVERT: A 130 MET cc_start: 0.9362 (mmm) cc_final: 0.9086 (mmt) REVERT: A 141 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8369 (mmtm) REVERT: A 158 TRP cc_start: 0.8308 (t-100) cc_final: 0.7872 (t60) REVERT: A 205 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 214 THR cc_start: 0.8345 (p) cc_final: 0.8074 (t) REVERT: A 220 ASP cc_start: 0.9230 (t70) cc_final: 0.8942 (t70) REVERT: A 239 MET cc_start: 0.8715 (tpp) cc_final: 0.8399 (tpp) REVERT: A 352 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8556 (t) REVERT: A 377 MET cc_start: 0.8712 (mpp) cc_final: 0.8391 (mpp) REVERT: B 20 TRP cc_start: 0.8808 (t-100) cc_final: 0.8534 (t-100) REVERT: B 83 LEU cc_start: 0.8713 (mm) cc_final: 0.8486 (mm) REVERT: B 84 ASN cc_start: 0.8921 (t0) cc_final: 0.8642 (t0) REVERT: B 110 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8460 (tp30) REVERT: B 130 MET cc_start: 0.9412 (mmm) cc_final: 0.8984 (mpp) REVERT: B 141 LYS cc_start: 0.8648 (mtmt) cc_final: 0.8391 (mmtm) REVERT: B 205 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 352 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8261 (t) REVERT: B 377 MET cc_start: 0.8904 (mmm) cc_final: 0.8363 (mpp) REVERT: C 54 TYR cc_start: 0.8043 (t80) cc_final: 0.7816 (t80) REVERT: C 110 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8902 (tm-30) REVERT: C 128 TYR cc_start: 0.8753 (t80) cc_final: 0.8318 (t80) REVERT: C 158 TRP cc_start: 0.8297 (t-100) cc_final: 0.7511 (m-10) REVERT: C 198 ASN cc_start: 0.8368 (t0) cc_final: 0.7998 (t0) REVERT: C 205 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7697 (tm-30) REVERT: C 214 THR cc_start: 0.8466 (p) cc_final: 0.8158 (t) REVERT: C 222 MET cc_start: 0.8756 (tmm) cc_final: 0.8492 (tmm) REVERT: C 233 HIS cc_start: 0.8644 (t-90) cc_final: 0.8290 (t-90) REVERT: C 239 MET cc_start: 0.8884 (tpp) cc_final: 0.6941 (tpp) REVERT: C 242 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7802 (pp20) REVERT: C 342 TYR cc_start: 0.7266 (m-80) cc_final: 0.6916 (m-10) REVERT: C 352 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8529 (t) REVERT: C 377 MET cc_start: 0.8512 (mmt) cc_final: 0.8138 (mmt) REVERT: C 383 TYR cc_start: 0.8662 (t80) cc_final: 0.8037 (t80) REVERT: D 84 ASN cc_start: 0.8927 (t0) cc_final: 0.8684 (t0) REVERT: D 110 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8364 (tp30) REVERT: D 130 MET cc_start: 0.9343 (mmm) cc_final: 0.9138 (mmt) REVERT: D 157 MET cc_start: 0.8457 (tpt) cc_final: 0.7958 (ttm) REVERT: D 197 MET cc_start: 0.6122 (tpp) cc_final: 0.5808 (tpp) REVERT: D 205 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7960 (tm-30) REVERT: D 214 THR cc_start: 0.8609 (m) cc_final: 0.8366 (t) REVERT: D 239 MET cc_start: 0.8684 (tpp) cc_final: 0.8284 (tpp) REVERT: D 352 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8504 (t) REVERT: D 377 MET cc_start: 0.8560 (mpp) cc_final: 0.8253 (mpp) REVERT: D 382 MET cc_start: 0.8785 (tpp) cc_final: 0.8503 (tpt) outliers start: 40 outliers final: 25 residues processed: 304 average time/residue: 0.0826 time to fit residues: 39.5288 Evaluate side-chains 277 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 HIS D 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.101633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082899 restraints weight = 31886.148| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 4.35 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12252 Z= 0.153 Angle : 0.612 9.989 16612 Z= 0.312 Chirality : 0.039 0.172 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.485 14.842 1624 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.66 % Allowed : 22.01 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.98 (0.22), residues: 1476 helix: 2.61 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.11 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 43 TYR 0.022 0.002 TYR A 99 PHE 0.010 0.001 PHE B 92 TRP 0.019 0.002 TRP C 20 HIS 0.007 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00333 (12252) covalent geometry : angle 0.61235 (16612) hydrogen bonds : bond 0.04992 ( 972) hydrogen bonds : angle 3.52132 ( 2892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 250 time to evaluate : 0.355 Fit side-chains REVERT: A 83 LEU cc_start: 0.8642 (mm) cc_final: 0.8424 (mm) REVERT: A 110 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8413 (tp30) REVERT: A 130 MET cc_start: 0.9430 (mmm) cc_final: 0.9202 (mmt) REVERT: A 141 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8302 (pttp) REVERT: A 158 TRP cc_start: 0.8317 (t-100) cc_final: 0.7943 (t60) REVERT: A 197 MET cc_start: 0.6779 (tpp) cc_final: 0.6548 (tpp) REVERT: A 205 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 214 THR cc_start: 0.8361 (p) cc_final: 0.8049 (t) REVERT: A 352 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8571 (t) REVERT: B 84 ASN cc_start: 0.9020 (t0) cc_final: 0.8706 (t0) REVERT: B 95 SER cc_start: 0.9427 (p) cc_final: 0.9159 (p) REVERT: B 110 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8500 (tp30) REVERT: B 130 MET cc_start: 0.9419 (mmm) cc_final: 0.9141 (mmt) REVERT: B 141 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8287 (pttp) REVERT: B 157 MET cc_start: 0.8299 (tpt) cc_final: 0.8014 (ttm) REVERT: B 205 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8157 (tm-30) REVERT: B 377 MET cc_start: 0.8969 (mmm) cc_final: 0.8388 (mpp) REVERT: C 29 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8586 (mpp80) REVERT: C 54 TYR cc_start: 0.8191 (t80) cc_final: 0.7978 (t80) REVERT: C 95 SER cc_start: 0.9395 (p) cc_final: 0.9147 (p) REVERT: C 110 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8946 (tm-30) REVERT: C 128 TYR cc_start: 0.8737 (t80) cc_final: 0.8323 (t80) REVERT: C 198 ASN cc_start: 0.8497 (t0) cc_final: 0.8008 (t0) REVERT: C 205 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7658 (tm-30) REVERT: C 214 THR cc_start: 0.8463 (p) cc_final: 0.8124 (t) REVERT: C 222 MET cc_start: 0.8871 (tmm) cc_final: 0.8534 (tmm) REVERT: C 233 HIS cc_start: 0.8776 (t-90) cc_final: 0.8342 (t-90) REVERT: C 239 MET cc_start: 0.8922 (tpp) cc_final: 0.6945 (tpp) REVERT: C 242 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7809 (pp20) REVERT: C 342 TYR cc_start: 0.7479 (m-80) cc_final: 0.6897 (m-10) REVERT: C 352 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8628 (t) REVERT: C 377 MET cc_start: 0.8663 (mmt) cc_final: 0.8332 (mmt) REVERT: C 383 TYR cc_start: 0.8700 (t80) cc_final: 0.8062 (t80) REVERT: D 83 LEU cc_start: 0.8856 (mm) cc_final: 0.8640 (mm) REVERT: D 84 ASN cc_start: 0.8955 (t0) cc_final: 0.8649 (t0) REVERT: D 110 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8399 (tp30) REVERT: D 130 MET cc_start: 0.9350 (mmm) cc_final: 0.9128 (mmt) REVERT: D 157 MET cc_start: 0.8519 (tpt) cc_final: 0.8018 (ttm) REVERT: D 158 TRP cc_start: 0.8397 (t-100) cc_final: 0.7646 (t60) REVERT: D 197 MET cc_start: 0.6191 (tpp) cc_final: 0.5825 (tpp) REVERT: D 205 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7413 (tm-30) REVERT: D 377 MET cc_start: 0.8621 (mpp) cc_final: 0.8311 (mpp) REVERT: D 382 MET cc_start: 0.8659 (tpp) cc_final: 0.8427 (tpt) REVERT: D 433 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8604 (tm-30) outliers start: 49 outliers final: 30 residues processed: 289 average time/residue: 0.0830 time to fit residues: 37.8746 Evaluate side-chains 264 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 90 optimal weight: 0.0870 chunk 114 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.104014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085507 restraints weight = 31029.229| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 4.26 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12252 Z= 0.132 Angle : 0.605 10.297 16612 Z= 0.305 Chirality : 0.039 0.173 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.472 14.433 1624 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.43 % Allowed : 23.43 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.22), residues: 1476 helix: 2.71 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.05 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 431 TYR 0.021 0.001 TYR A 99 PHE 0.018 0.001 PHE D 92 TRP 0.025 0.002 TRP C 20 HIS 0.002 0.000 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00276 (12252) covalent geometry : angle 0.60518 (16612) hydrogen bonds : bond 0.04726 ( 972) hydrogen bonds : angle 3.42310 ( 2892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8600 (mm) cc_final: 0.8361 (mm) REVERT: A 94 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8199 (mm-40) REVERT: A 95 SER cc_start: 0.9346 (p) cc_final: 0.8962 (p) REVERT: A 141 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8209 (pttp) REVERT: A 158 TRP cc_start: 0.8292 (t-100) cc_final: 0.8044 (t60) REVERT: A 160 LEU cc_start: 0.8631 (tt) cc_final: 0.8252 (mp) REVERT: A 197 MET cc_start: 0.6724 (tpp) cc_final: 0.6449 (tpp) REVERT: A 205 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 214 THR cc_start: 0.8325 (p) cc_final: 0.8022 (t) REVERT: A 220 ASP cc_start: 0.9119 (t70) cc_final: 0.8750 (t0) REVERT: A 352 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8546 (t) REVERT: B 84 ASN cc_start: 0.9117 (t0) cc_final: 0.8799 (t0) REVERT: B 92 PHE cc_start: 0.8505 (m-80) cc_final: 0.8143 (m-80) REVERT: B 110 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8836 (tp30) REVERT: B 141 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8179 (pttp) REVERT: B 157 MET cc_start: 0.8279 (tpt) cc_final: 0.7891 (ttm) REVERT: B 158 TRP cc_start: 0.8150 (t-100) cc_final: 0.7697 (t60) REVERT: B 205 GLU cc_start: 0.8568 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 377 MET cc_start: 0.8951 (mmm) cc_final: 0.8378 (mpp) REVERT: B 379 LEU cc_start: 0.8082 (tp) cc_final: 0.7707 (tp) REVERT: C 29 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8566 (mpp80) REVERT: C 54 TYR cc_start: 0.8132 (t80) cc_final: 0.7929 (t80) REVERT: C 94 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8167 (tp40) REVERT: C 110 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8920 (tm-30) REVERT: C 128 TYR cc_start: 0.8751 (t80) cc_final: 0.8404 (t80) REVERT: C 158 TRP cc_start: 0.8166 (t-100) cc_final: 0.7709 (m-10) REVERT: C 198 ASN cc_start: 0.8505 (t0) cc_final: 0.7997 (t0) REVERT: C 205 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 214 THR cc_start: 0.8450 (p) cc_final: 0.8159 (t) REVERT: C 222 MET cc_start: 0.8827 (tmm) cc_final: 0.8524 (tmm) REVERT: C 239 MET cc_start: 0.8916 (tpp) cc_final: 0.6870 (tpp) REVERT: C 242 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7779 (pp20) REVERT: C 342 TYR cc_start: 0.7330 (m-80) cc_final: 0.6729 (m-10) REVERT: C 352 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8682 (t) REVERT: D 29 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8462 (mpp80) REVERT: D 83 LEU cc_start: 0.8841 (mm) cc_final: 0.8630 (mm) REVERT: D 84 ASN cc_start: 0.8917 (t0) cc_final: 0.8411 (t0) REVERT: D 158 TRP cc_start: 0.8308 (t-100) cc_final: 0.7673 (t60) REVERT: D 160 LEU cc_start: 0.8627 (tt) cc_final: 0.8212 (mp) REVERT: D 197 MET cc_start: 0.6206 (tpp) cc_final: 0.5832 (tpp) REVERT: D 205 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7479 (tm-30) REVERT: D 232 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 336 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8885 (pp20) REVERT: D 377 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8301 (mpp) REVERT: D 426 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8537 (tp-100) REVERT: D 433 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8619 (tm-30) outliers start: 46 outliers final: 26 residues processed: 290 average time/residue: 0.0873 time to fit residues: 39.5828 Evaluate side-chains 270 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 36 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 198 ASN ** 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 = 0.3760 r_free = 0.3760 target = 0.103415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084802 restraints weight = 30935.311| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.30 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12252 Z= 0.144 Angle : 0.635 9.321 16612 Z= 0.317 Chirality : 0.039 0.180 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.452 14.996 1624 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.81 % Allowed : 24.70 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.18 (0.22), residues: 1476 helix: 2.75 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.03 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 37 TYR 0.025 0.002 TYR A 99 PHE 0.015 0.001 PHE B 92 TRP 0.028 0.002 TRP C 20 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00313 (12252) covalent geometry : angle 0.63510 (16612) hydrogen bonds : bond 0.04817 ( 972) hydrogen bonds : angle 3.47153 ( 2892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 251 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8058 (mm-40) REVERT: A 110 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8429 (tp30) REVERT: A 158 TRP cc_start: 0.8341 (t-100) cc_final: 0.8040 (t60) REVERT: A 160 LEU cc_start: 0.8650 (tt) cc_final: 0.8269 (mp) REVERT: A 197 MET cc_start: 0.6735 (tpp) cc_final: 0.6421 (tpp) REVERT: A 205 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7447 (tm-30) REVERT: A 220 ASP cc_start: 0.9181 (t70) cc_final: 0.8954 (t0) REVERT: A 352 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8523 (t) REVERT: A 377 MET cc_start: 0.8883 (mmm) cc_final: 0.8676 (mmt) REVERT: B 83 LEU cc_start: 0.8967 (mm) cc_final: 0.8762 (mm) REVERT: B 84 ASN cc_start: 0.9081 (t0) cc_final: 0.8801 (t0) REVERT: B 94 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8292 (tp-100) REVERT: B 110 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8847 (tp30) REVERT: B 157 MET cc_start: 0.8286 (tpt) cc_final: 0.7842 (ttm) REVERT: B 158 TRP cc_start: 0.8173 (t-100) cc_final: 0.7724 (t60) REVERT: B 205 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 377 MET cc_start: 0.8999 (mmm) cc_final: 0.8430 (mpp) REVERT: B 458 MET cc_start: 0.8939 (tpp) cc_final: 0.8694 (tpt) REVERT: C 29 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8568 (mpp80) REVERT: C 54 TYR cc_start: 0.8187 (t80) cc_final: 0.7955 (t80) REVERT: C 94 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8099 (tp40) REVERT: C 95 SER cc_start: 0.9422 (p) cc_final: 0.9191 (p) REVERT: C 110 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8955 (tm-30) REVERT: C 128 TYR cc_start: 0.8732 (t80) cc_final: 0.8296 (t80) REVERT: C 157 MET cc_start: 0.7693 (tpt) cc_final: 0.7360 (ttp) REVERT: C 198 ASN cc_start: 0.8490 (t0) cc_final: 0.8027 (t0) REVERT: C 205 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7732 (tm-30) REVERT: C 214 THR cc_start: 0.8427 (p) cc_final: 0.8115 (t) REVERT: C 222 MET cc_start: 0.8858 (tmm) cc_final: 0.8525 (tmm) REVERT: C 239 MET cc_start: 0.8917 (tpp) cc_final: 0.6933 (tpp) REVERT: C 242 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7804 (pp20) REVERT: C 342 TYR cc_start: 0.7332 (m-80) cc_final: 0.6614 (m-10) REVERT: D 29 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8249 (mtp85) REVERT: D 83 LEU cc_start: 0.8813 (mm) cc_final: 0.8607 (mm) REVERT: D 84 ASN cc_start: 0.8906 (t0) cc_final: 0.8444 (t0) REVERT: D 157 MET cc_start: 0.8200 (tpt) cc_final: 0.7994 (ttm) REVERT: D 158 TRP cc_start: 0.8329 (t-100) cc_final: 0.7866 (t60) REVERT: D 160 LEU cc_start: 0.8656 (tt) cc_final: 0.8267 (mp) REVERT: D 197 MET cc_start: 0.6281 (tpp) cc_final: 0.5890 (tpp) REVERT: D 205 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7387 (tm-30) REVERT: D 232 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7759 (tm-30) REVERT: D 426 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8603 (tp-100) REVERT: D 433 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8592 (tm-30) outliers start: 51 outliers final: 33 residues processed: 288 average time/residue: 0.0854 time to fit residues: 38.0872 Evaluate side-chains 274 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 95 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 ASN ** 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 = 0.3689 r_free = 0.3689 target = 0.101183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.082356 restraints weight = 32259.783| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.42 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12252 Z= 0.145 Angle : 0.654 9.486 16612 Z= 0.325 Chirality : 0.040 0.182 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.450 15.607 1624 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.58 % Allowed : 25.22 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.26 (0.22), residues: 1476 helix: 2.80 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 431 TYR 0.028 0.002 TYR A 99 PHE 0.018 0.001 PHE C 92 TRP 0.030 0.002 TRP C 20 HIS 0.002 0.000 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00318 (12252) covalent geometry : angle 0.65434 (16612) hydrogen bonds : bond 0.04885 ( 972) hydrogen bonds : angle 3.48347 ( 2892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8058 (mm-40) REVERT: A 158 TRP cc_start: 0.8295 (t-100) cc_final: 0.8092 (t60) REVERT: A 160 LEU cc_start: 0.8657 (tt) cc_final: 0.8289 (mp) REVERT: A 197 MET cc_start: 0.6859 (tpp) cc_final: 0.6564 (tpp) REVERT: A 205 GLU cc_start: 0.8483 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 220 ASP cc_start: 0.9224 (t70) cc_final: 0.8952 (t0) REVERT: A 352 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8483 (t) REVERT: A 377 MET cc_start: 0.8840 (mmm) cc_final: 0.8581 (mmt) REVERT: B 84 ASN cc_start: 0.9146 (t0) cc_final: 0.8693 (t0) REVERT: B 94 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8201 (tp-100) REVERT: B 95 SER cc_start: 0.9423 (p) cc_final: 0.9147 (p) REVERT: B 157 MET cc_start: 0.8372 (tpt) cc_final: 0.7972 (ttm) REVERT: B 158 TRP cc_start: 0.8073 (t-100) cc_final: 0.7781 (t60) REVERT: B 160 LEU cc_start: 0.8633 (tt) cc_final: 0.8233 (mp) REVERT: B 205 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 377 MET cc_start: 0.9016 (mmm) cc_final: 0.8442 (mpp) REVERT: B 458 MET cc_start: 0.8907 (tpp) cc_final: 0.8645 (tpt) REVERT: C 29 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8613 (mpp80) REVERT: C 95 SER cc_start: 0.9464 (p) cc_final: 0.9188 (p) REVERT: C 110 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8963 (tm-30) REVERT: C 130 MET cc_start: 0.9311 (mmm) cc_final: 0.8850 (mpp) REVERT: C 157 MET cc_start: 0.7726 (tpt) cc_final: 0.7393 (ttp) REVERT: C 198 ASN cc_start: 0.8458 (t0) cc_final: 0.8024 (t0) REVERT: C 205 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7873 (tm-30) REVERT: C 214 THR cc_start: 0.8513 (p) cc_final: 0.8189 (t) REVERT: C 222 MET cc_start: 0.8854 (tmm) cc_final: 0.8568 (tmm) REVERT: C 239 MET cc_start: 0.8920 (tpp) cc_final: 0.7029 (tpp) REVERT: C 242 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7819 (pp20) REVERT: C 383 TYR cc_start: 0.8655 (t80) cc_final: 0.8136 (t80) REVERT: D 29 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8228 (mtp85) REVERT: D 84 ASN cc_start: 0.8939 (t0) cc_final: 0.8442 (t0) REVERT: D 87 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7279 (t) REVERT: D 94 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8277 (tp40) REVERT: D 157 MET cc_start: 0.8237 (tpt) cc_final: 0.7788 (ttm) REVERT: D 160 LEU cc_start: 0.8644 (tt) cc_final: 0.8271 (mp) REVERT: D 197 MET cc_start: 0.6342 (tpp) cc_final: 0.5954 (tpp) REVERT: D 205 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7924 (tm-30) REVERT: D 232 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7766 (tm-30) REVERT: D 377 MET cc_start: 0.8885 (mmt) cc_final: 0.8343 (mpp) REVERT: D 426 GLN cc_start: 0.9067 (tp-100) cc_final: 0.8613 (tp-100) REVERT: D 433 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8586 (tm-30) outliers start: 48 outliers final: 29 residues processed: 288 average time/residue: 0.0912 time to fit residues: 40.2074 Evaluate side-chains 266 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080573 restraints weight = 32666.743| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.41 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12252 Z= 0.178 Angle : 0.713 9.633 16612 Z= 0.356 Chirality : 0.041 0.179 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.529 16.090 1624 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.43 % Allowed : 25.82 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.21 (0.22), residues: 1476 helix: 2.77 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.04 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.033 0.002 TYR A 99 PHE 0.029 0.001 PHE D 92 TRP 0.036 0.002 TRP C 20 HIS 0.003 0.001 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00398 (12252) covalent geometry : angle 0.71250 (16612) hydrogen bonds : bond 0.05265 ( 972) hydrogen bonds : angle 3.61445 ( 2892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8077 (mm-40) REVERT: A 110 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8394 (tp30) REVERT: A 160 LEU cc_start: 0.8641 (tt) cc_final: 0.8265 (mp) REVERT: A 197 MET cc_start: 0.6882 (tpp) cc_final: 0.6575 (tpp) REVERT: A 205 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 214 THR cc_start: 0.8563 (t) cc_final: 0.8358 (t) REVERT: A 352 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8558 (t) REVERT: A 377 MET cc_start: 0.8781 (mmm) cc_final: 0.8550 (mmt) REVERT: A 433 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8708 (tm-30) REVERT: B 84 ASN cc_start: 0.9250 (t0) cc_final: 0.8931 (t0) REVERT: B 94 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8267 (tp-100) REVERT: B 118 GLU cc_start: 0.8725 (pm20) cc_final: 0.8229 (pm20) REVERT: B 160 LEU cc_start: 0.8675 (tt) cc_final: 0.8269 (mp) REVERT: B 205 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 232 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 377 MET cc_start: 0.9100 (mmm) cc_final: 0.8469 (mpp) REVERT: C 95 SER cc_start: 0.9446 (p) cc_final: 0.9151 (p) REVERT: C 110 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8926 (tm-30) REVERT: C 157 MET cc_start: 0.7791 (tpt) cc_final: 0.7566 (ttp) REVERT: C 198 ASN cc_start: 0.8458 (t0) cc_final: 0.8008 (t0) REVERT: C 205 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 214 THR cc_start: 0.8518 (p) cc_final: 0.8163 (t) REVERT: C 222 MET cc_start: 0.8887 (tmm) cc_final: 0.8578 (tmm) REVERT: C 239 MET cc_start: 0.8908 (tpp) cc_final: 0.7035 (tpp) REVERT: C 242 GLU cc_start: 0.8561 (pp20) cc_final: 0.7851 (pp20) REVERT: D 29 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8312 (mtp85) REVERT: D 84 ASN cc_start: 0.9161 (t0) cc_final: 0.8857 (t0) REVERT: D 94 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8272 (tp40) REVERT: D 157 MET cc_start: 0.8239 (tpt) cc_final: 0.7820 (ttm) REVERT: D 160 LEU cc_start: 0.8610 (tt) cc_final: 0.8251 (mp) REVERT: D 197 MET cc_start: 0.6483 (tpp) cc_final: 0.6098 (tpp) REVERT: D 205 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8014 (tm-30) REVERT: D 232 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7762 (tm-30) REVERT: D 377 MET cc_start: 0.8844 (mmt) cc_final: 0.8265 (mpp) REVERT: D 426 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8681 (tp-100) REVERT: D 433 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8528 (tm-30) outliers start: 46 outliers final: 29 residues processed: 275 average time/residue: 0.0858 time to fit residues: 36.9415 Evaluate side-chains 265 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 131 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 ASN C 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.100707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082414 restraints weight = 32268.782| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.38 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12252 Z= 0.147 Angle : 0.706 9.696 16612 Z= 0.349 Chirality : 0.040 0.177 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.520 16.663 1624 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.24 % Allowed : 27.39 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.27 (0.22), residues: 1476 helix: 2.79 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.93 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.028 0.002 TYR A 99 PHE 0.009 0.001 PHE C 183 TRP 0.034 0.002 TRP A 20 HIS 0.002 0.000 HIS D 407 Details of bonding type rmsd covalent geometry : bond 0.00324 (12252) covalent geometry : angle 0.70590 (16612) hydrogen bonds : bond 0.04906 ( 972) hydrogen bonds : angle 3.51210 ( 2892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8033 (mm-40) REVERT: A 95 SER cc_start: 0.9341 (p) cc_final: 0.8961 (p) REVERT: A 158 TRP cc_start: 0.8268 (t-100) cc_final: 0.8059 (t60) REVERT: A 160 LEU cc_start: 0.8610 (tt) cc_final: 0.8272 (mp) REVERT: A 197 MET cc_start: 0.6864 (tpp) cc_final: 0.6583 (tpp) REVERT: A 205 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7468 (tm-30) REVERT: A 352 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8504 (t) REVERT: A 377 MET cc_start: 0.8732 (mmm) cc_final: 0.8489 (mmt) REVERT: A 382 MET cc_start: 0.8601 (tpp) cc_final: 0.8367 (tpt) REVERT: A 433 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8766 (tm-30) REVERT: B 84 ASN cc_start: 0.9127 (t0) cc_final: 0.8880 (t0) REVERT: B 94 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8214 (tp40) REVERT: B 110 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8814 (tm-30) REVERT: B 158 TRP cc_start: 0.8175 (t-100) cc_final: 0.7851 (t60) REVERT: B 160 LEU cc_start: 0.8653 (tt) cc_final: 0.8231 (mp) REVERT: B 197 MET cc_start: 0.6999 (ttp) cc_final: 0.6707 (ttp) REVERT: B 205 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 232 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 110 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8908 (tm-30) REVERT: C 157 MET cc_start: 0.7704 (tpt) cc_final: 0.7436 (ttp) REVERT: C 198 ASN cc_start: 0.8471 (t0) cc_final: 0.8034 (t0) REVERT: C 205 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 214 THR cc_start: 0.8490 (p) cc_final: 0.8136 (t) REVERT: C 222 MET cc_start: 0.8832 (tmm) cc_final: 0.8598 (tmm) REVERT: C 239 MET cc_start: 0.8895 (tpp) cc_final: 0.7015 (tpp) REVERT: C 242 GLU cc_start: 0.8500 (pp20) cc_final: 0.7760 (pp20) REVERT: D 29 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8238 (mtp85) REVERT: D 84 ASN cc_start: 0.9098 (t0) cc_final: 0.8804 (t0) REVERT: D 94 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8280 (tp40) REVERT: D 157 MET cc_start: 0.8224 (tpt) cc_final: 0.7796 (ttm) REVERT: D 160 LEU cc_start: 0.8635 (tt) cc_final: 0.8245 (mp) REVERT: D 197 MET cc_start: 0.6522 (tpp) cc_final: 0.6126 (tpp) REVERT: D 205 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7971 (tm-30) REVERT: D 232 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7796 (tm-30) REVERT: D 377 MET cc_start: 0.8851 (mmt) cc_final: 0.8261 (mpp) REVERT: D 426 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8631 (tp-100) REVERT: D 433 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8540 (tm-30) outliers start: 30 outliers final: 26 residues processed: 267 average time/residue: 0.0850 time to fit residues: 35.6136 Evaluate side-chains 252 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 446 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 26 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS C 433 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.102238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083247 restraints weight = 32279.544| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.50 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12252 Z= 0.144 Angle : 0.710 9.763 16612 Z= 0.348 Chirality : 0.040 0.169 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.515 17.266 1624 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.84 % Allowed : 26.72 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.33 (0.22), residues: 1476 helix: 2.83 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.031 0.002 TYR D 99 PHE 0.010 0.001 PHE C 183 TRP 0.036 0.002 TRP C 20 HIS 0.006 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00319 (12252) covalent geometry : angle 0.71015 (16612) hydrogen bonds : bond 0.04738 ( 972) hydrogen bonds : angle 3.46457 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.10 seconds wall clock time: 35 minutes 58.13 seconds (2158.13 seconds total)