Starting phenix.real_space_refine on Thu Sep 26 03:37:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/09_2024/7lic_23372.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/09_2024/7lic_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/09_2024/7lic_23372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/09_2024/7lic_23372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/09_2024/7lic_23372.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/09_2024/7lic_23372.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: C, B, D Time building chain proxies: 6.31, per 1000 atoms: 0.53 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: 3.41 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.92 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: 3.53 Time building geometry restraints manager: 3.52 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: 0.00 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 27.920 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- 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= 0.254 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 : 5.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (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 TRP 0.018 0.002 TRP D 155 HIS 0.004 0.001 HIS B 420 PHE 0.011 0.001 PHE D 450 TYR 0.017 0.002 TYR D 204 ARG 0.002 0.000 ARG B 422 *********************** 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 fitting. rotamer outliers: 12 poor density : 406 time to evaluate : 1.234 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: 0.2159 time to fit residues: 129.4864 Evaluate side-chains 233 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 229 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 124 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12252 Z= 0.206 Angle : 0.620 6.389 16612 Z= 0.324 Chirality : 0.038 0.138 1992 Planarity : 0.005 0.047 1988 Dihedral : 3.950 14.347 1628 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.46 % Allowed : 14.85 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.22), residues: 1476 helix: 1.76 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 155 HIS 0.005 0.001 HIS B 233 PHE 0.012 0.001 PHE C 450 TYR 0.020 0.002 TYR A 362 ARG 0.008 0.000 ARG C 43 *********************** 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 318 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 285 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.9255 (tp) cc_final: 0.9006 (tp) REVERT: A 110 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7832 (tp30) REVERT: A 158 TRP cc_start: 0.7971 (t-100) cc_final: 0.7605 (m-10) REVERT: A 205 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 233 HIS cc_start: 0.8142 (t-90) cc_final: 0.7910 (t70) REVERT: A 377 MET cc_start: 0.8447 (mpp) cc_final: 0.8093 (mpp) REVERT: A 394 LEU cc_start: 0.9252 (mt) cc_final: 0.9039 (mt) REVERT: A 419 ASP cc_start: 0.7705 (p0) cc_final: 0.7476 (p0) REVERT: A 465 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8471 (tt) REVERT: B 110 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7823 (tp30) REVERT: B 205 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 419 ASP cc_start: 0.7776 (p0) cc_final: 0.7553 (p0) REVERT: B 465 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8480 (tt) REVERT: C 17 LEU cc_start: 0.9431 (tt) cc_final: 0.9162 (pp) REVERT: C 54 TYR cc_start: 0.8243 (t80) cc_final: 0.8001 (t80) REVERT: C 128 TYR cc_start: 0.8454 (t80) cc_final: 0.8191 (t80) REVERT: C 158 TRP cc_start: 0.7999 (t-100) cc_final: 0.7549 (m100) REVERT: C 198 ASN cc_start: 0.8196 (t0) cc_final: 0.7753 (t0) REVERT: C 205 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 214 THR cc_start: 0.8802 (p) cc_final: 0.8467 (t) REVERT: C 239 MET cc_start: 0.8344 (tpp) cc_final: 0.8101 (tpp) REVERT: C 419 ASP cc_start: 0.7705 (p0) cc_final: 0.7474 (p0) REVERT: C 465 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8730 (mm) REVERT: D 110 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7808 (tp30) REVERT: D 136 THR cc_start: 0.9487 (p) cc_final: 0.9266 (p) REVERT: D 158 TRP cc_start: 0.7977 (t-100) cc_final: 0.7723 (m-10) REVERT: D 205 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7900 (tm-30) REVERT: D 214 THR cc_start: 0.8695 (m) cc_final: 0.8426 (t) REVERT: D 377 MET cc_start: 0.8526 (mpp) cc_final: 0.8198 (mpp) REVERT: D 465 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8465 (tt) outliers start: 33 outliers final: 13 residues processed: 303 average time/residue: 0.1897 time to fit residues: 88.0058 Evaluate side-chains 250 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 465 LEU 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 415 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 465 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 Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12252 Z= 0.195 Angle : 0.596 8.555 16612 Z= 0.309 Chirality : 0.038 0.156 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.714 15.909 1624 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.06 % Allowed : 18.13 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.22), residues: 1476 helix: 2.29 (0.15), residues: 1208 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 20 HIS 0.006 0.001 HIS B 233 PHE 0.011 0.001 PHE B 450 TYR 0.020 0.002 TYR C 204 ARG 0.004 0.000 ARG A 107 *********************** 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 306 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 265 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.9295 (p) cc_final: 0.9035 (p) REVERT: A 110 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7812 (tp30) REVERT: A 205 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 214 THR cc_start: 0.8560 (t) cc_final: 0.8327 (t) REVERT: A 352 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8773 (t) REVERT: A 377 MET cc_start: 0.8429 (mpp) cc_final: 0.8099 (mpp) REVERT: A 394 LEU cc_start: 0.9216 (mt) cc_final: 0.8988 (mt) REVERT: A 419 ASP cc_start: 0.7704 (p0) cc_final: 0.7475 (p0) REVERT: A 465 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8452 (tt) REVERT: B 110 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7962 (tp30) REVERT: B 141 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8558 (pttp) REVERT: B 197 MET cc_start: 0.6896 (tpp) cc_final: 0.6688 (tpp) REVERT: B 205 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 377 MET cc_start: 0.8694 (mmm) cc_final: 0.8270 (mpp) REVERT: B 419 ASP cc_start: 0.7806 (p0) cc_final: 0.7523 (p0) REVERT: B 465 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8473 (tt) REVERT: C 29 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8391 (mpp80) REVERT: C 54 TYR cc_start: 0.8244 (t80) cc_final: 0.8036 (t80) REVERT: C 95 SER cc_start: 0.9369 (p) cc_final: 0.9105 (p) REVERT: C 128 TYR cc_start: 0.8524 (t80) cc_final: 0.8198 (t80) REVERT: C 205 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7773 (tm-30) REVERT: C 214 THR cc_start: 0.8726 (p) cc_final: 0.8391 (t) REVERT: C 239 MET cc_start: 0.8436 (tpp) cc_final: 0.6254 (tpp) REVERT: C 242 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7703 (pp20) REVERT: C 383 TYR cc_start: 0.8631 (t80) cc_final: 0.8103 (t80) REVERT: C 419 ASP cc_start: 0.7788 (p0) cc_final: 0.7503 (p0) REVERT: C 465 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8716 (mm) REVERT: D 110 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7834 (tp30) REVERT: D 158 TRP cc_start: 0.7956 (t-100) cc_final: 0.7668 (m-10) REVERT: D 197 MET cc_start: 0.6479 (tpp) cc_final: 0.6201 (tpp) REVERT: D 205 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7903 (tm-30) REVERT: D 352 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8830 (t) REVERT: D 377 MET cc_start: 0.8451 (mpp) cc_final: 0.8183 (mpp) REVERT: D 465 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8427 (tt) outliers start: 41 outliers final: 21 residues processed: 298 average time/residue: 0.1913 time to fit residues: 86.6643 Evaluate side-chains 267 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 238 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 465 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 355 LEU 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 B residue 465 LEU 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 242 GLU 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 109 LEU Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 0.0970 chunk 14 optimal weight: 0.0170 chunk 64 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS B 233 HIS ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 ASN C 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3606 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= 0.171 Angle : 0.578 7.799 16612 Z= 0.295 Chirality : 0.038 0.160 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.592 15.139 1624 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.99 % Allowed : 20.00 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.22), residues: 1476 helix: 2.54 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 20 HIS 0.005 0.001 HIS A 233 PHE 0.008 0.001 PHE B 450 TYR 0.026 0.001 TYR B 99 ARG 0.003 0.000 ARG A 107 *********************** 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 315 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 275 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9332 (p) cc_final: 0.9104 (p) REVERT: A 110 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7877 (tp30) REVERT: A 197 MET cc_start: 0.6977 (tpp) cc_final: 0.6430 (tpp) REVERT: A 205 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 214 THR cc_start: 0.8540 (t) cc_final: 0.8302 (t) REVERT: A 377 MET cc_start: 0.8451 (mpp) cc_final: 0.8230 (mpp) REVERT: A 382 MET cc_start: 0.8696 (tpp) cc_final: 0.8469 (tpt) REVERT: A 394 LEU cc_start: 0.9184 (mt) cc_final: 0.8716 (mt) REVERT: A 465 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8434 (tt) REVERT: B 92 PHE cc_start: 0.8681 (m-10) cc_final: 0.8288 (m-10) REVERT: B 110 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7939 (tp30) REVERT: B 141 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8444 (pttp) REVERT: B 197 MET cc_start: 0.6776 (tpp) cc_final: 0.6560 (tpp) REVERT: B 205 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8012 (tm-30) REVERT: B 220 ASP cc_start: 0.8552 (t70) cc_final: 0.8346 (t70) REVERT: B 377 MET cc_start: 0.8662 (mmm) cc_final: 0.8322 (mpp) REVERT: B 419 ASP cc_start: 0.7779 (p0) cc_final: 0.7546 (p0) REVERT: B 465 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8460 (tt) REVERT: C 95 SER cc_start: 0.9344 (p) cc_final: 0.9114 (p) REVERT: C 128 TYR cc_start: 0.8517 (t80) cc_final: 0.8212 (t80) REVERT: C 205 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 214 THR cc_start: 0.8586 (p) cc_final: 0.8282 (t) REVERT: C 239 MET cc_start: 0.8413 (tpp) cc_final: 0.6253 (tpp) REVERT: C 242 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: C 383 TYR cc_start: 0.8631 (t80) cc_final: 0.8017 (t80) REVERT: C 419 ASP cc_start: 0.7784 (p0) cc_final: 0.7544 (p0) REVERT: C 465 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8708 (mm) REVERT: D 20 TRP cc_start: 0.8524 (t-100) cc_final: 0.8172 (t-100) REVERT: D 105 ASN cc_start: 0.8473 (m-40) cc_final: 0.8122 (m110) REVERT: D 110 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7862 (tp30) REVERT: D 158 TRP cc_start: 0.7933 (t-100) cc_final: 0.7724 (t60) REVERT: D 197 MET cc_start: 0.6585 (tpp) cc_final: 0.6261 (tpp) REVERT: D 205 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7272 (tm-30) REVERT: D 352 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8793 (t) REVERT: D 377 MET cc_start: 0.8389 (mpp) cc_final: 0.8148 (mpp) REVERT: D 382 MET cc_start: 0.8679 (tpp) cc_final: 0.8439 (tpt) REVERT: D 465 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8427 (tt) outliers start: 40 outliers final: 18 residues processed: 302 average time/residue: 0.1920 time to fit residues: 87.8541 Evaluate side-chains 268 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 244 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 465 LEU 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 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 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.0470 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 HIS D 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12252 Z= 0.178 Angle : 0.595 8.188 16612 Z= 0.301 Chirality : 0.038 0.173 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.502 15.474 1624 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.91 % Allowed : 21.64 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.22), residues: 1476 helix: 2.65 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.35 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 20 HIS 0.007 0.001 HIS D 233 PHE 0.011 0.001 PHE C 92 TYR 0.021 0.002 TYR D 99 ARG 0.004 0.000 ARG C 43 *********************** 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 304 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 265 time to evaluate : 1.407 Fit side-chains REVERT: A 95 SER cc_start: 0.9316 (p) cc_final: 0.9071 (p) REVERT: A 110 GLU cc_start: 0.8527 (tm-30) cc_final: 0.7953 (tp30) REVERT: A 160 LEU cc_start: 0.8576 (tt) cc_final: 0.8204 (mp) REVERT: A 214 THR cc_start: 0.8531 (t) cc_final: 0.8233 (t) REVERT: A 336 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7994 (pp20) REVERT: A 465 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8405 (tt) REVERT: B 110 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7962 (tp30) REVERT: B 197 MET cc_start: 0.6862 (tpp) cc_final: 0.6568 (tpp) REVERT: B 205 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7576 (tm-30) REVERT: B 220 ASP cc_start: 0.8672 (t70) cc_final: 0.8440 (t70) REVERT: B 377 MET cc_start: 0.8760 (mmm) cc_final: 0.8381 (mpp) REVERT: B 419 ASP cc_start: 0.7797 (p0) cc_final: 0.7547 (p0) REVERT: B 465 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8412 (tt) REVERT: C 95 SER cc_start: 0.9338 (p) cc_final: 0.9119 (p) REVERT: C 128 TYR cc_start: 0.8458 (t80) cc_final: 0.8185 (t80) REVERT: C 198 ASN cc_start: 0.8590 (t0) cc_final: 0.8187 (t0) REVERT: C 205 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 214 THR cc_start: 0.8563 (p) cc_final: 0.8252 (t) REVERT: C 239 MET cc_start: 0.8443 (tpp) cc_final: 0.6249 (tpp) REVERT: C 242 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7668 (pp20) REVERT: C 383 TYR cc_start: 0.8601 (t80) cc_final: 0.7862 (t80) REVERT: C 419 ASP cc_start: 0.7659 (p0) cc_final: 0.7364 (p0) REVERT: C 465 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8714 (mm) REVERT: D 20 TRP cc_start: 0.8596 (t-100) cc_final: 0.8258 (t-100) REVERT: D 94 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8650 (mm-40) REVERT: D 105 ASN cc_start: 0.8457 (m-40) cc_final: 0.8061 (m110) REVERT: D 197 MET cc_start: 0.6624 (tpp) cc_final: 0.6261 (tpp) REVERT: D 205 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7257 (tm-30) REVERT: D 352 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8767 (t) REVERT: D 377 MET cc_start: 0.8395 (mpp) cc_final: 0.8137 (mpp) REVERT: D 382 MET cc_start: 0.8696 (tpp) cc_final: 0.8467 (tpt) REVERT: D 433 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8258 (tm-30) REVERT: D 465 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8427 (tt) outliers start: 39 outliers final: 21 residues processed: 292 average time/residue: 0.1943 time to fit residues: 86.9464 Evaluate side-chains 266 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 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 415 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 242 GLU 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 C residue 465 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12252 Z= 0.260 Angle : 0.656 8.460 16612 Z= 0.337 Chirality : 0.040 0.181 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.561 15.014 1624 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.81 % Allowed : 23.36 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.22), residues: 1476 helix: 2.63 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.25 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 20 HIS 0.002 0.001 HIS A 420 PHE 0.019 0.001 PHE D 92 TYR 0.027 0.002 TYR A 99 ARG 0.004 0.001 ARG C 43 *********************** 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 291 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 1.314 Fit side-chains REVERT: A 95 SER cc_start: 0.9349 (p) cc_final: 0.9109 (p) REVERT: A 160 LEU cc_start: 0.8576 (tt) cc_final: 0.8204 (mp) REVERT: A 197 MET cc_start: 0.7237 (tpp) cc_final: 0.6735 (tpp) REVERT: A 214 THR cc_start: 0.8597 (t) cc_final: 0.8347 (t) REVERT: A 377 MET cc_start: 0.9026 (mmm) cc_final: 0.8704 (mpp) REVERT: A 465 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8389 (tt) REVERT: B 95 SER cc_start: 0.9415 (p) cc_final: 0.9158 (p) REVERT: B 110 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8031 (tp30) REVERT: B 197 MET cc_start: 0.6953 (tpp) cc_final: 0.6672 (tpp) REVERT: B 377 MET cc_start: 0.8912 (mmm) cc_final: 0.8418 (mpp) REVERT: B 465 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8431 (tt) REVERT: C 92 PHE cc_start: 0.8561 (m-80) cc_final: 0.8340 (m-80) REVERT: C 94 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8537 (tp40) REVERT: C 95 SER cc_start: 0.9375 (p) cc_final: 0.9153 (p) REVERT: C 198 ASN cc_start: 0.8644 (t0) cc_final: 0.8107 (t0) REVERT: C 205 GLU cc_start: 0.8113 (tm-30) cc_final: 0.6991 (tm-30) REVERT: C 214 THR cc_start: 0.8555 (p) cc_final: 0.8184 (t) REVERT: D 29 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8327 (mpp80) REVERT: D 94 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8643 (mm-40) REVERT: D 105 ASN cc_start: 0.8671 (m-40) cc_final: 0.8386 (m-40) REVERT: D 197 MET cc_start: 0.6753 (tpp) cc_final: 0.6335 (tpp) REVERT: D 232 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7566 (tm-30) REVERT: D 352 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8793 (t) REVERT: D 377 MET cc_start: 0.8478 (mpp) cc_final: 0.8203 (mpp) REVERT: D 433 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8193 (tm-30) REVERT: D 465 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8419 (tt) outliers start: 51 outliers final: 28 residues processed: 278 average time/residue: 0.1881 time to fit residues: 80.2385 Evaluate side-chains 260 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 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 420 HIS Chi-restraints excluded: chain B residue 465 LEU 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 388 ILE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 95 SER 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 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 120 optimal weight: 0.0370 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 89 optimal weight: 0.0030 chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.4868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12252 Z= 0.178 Angle : 0.648 11.677 16612 Z= 0.320 Chirality : 0.039 0.174 1992 Planarity : 0.004 0.043 1988 Dihedral : 3.490 14.882 1624 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.99 % Allowed : 24.78 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.22), residues: 1476 helix: 2.74 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 20 HIS 0.003 0.000 HIS A 33 PHE 0.014 0.001 PHE B 92 TYR 0.023 0.002 TYR A 99 ARG 0.003 0.000 ARG B 29 *********************** 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 fitting. rotamer outliers: 40 poor density : 262 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8515 (tp-100) REVERT: A 95 SER cc_start: 0.9324 (p) cc_final: 0.9083 (p) REVERT: A 110 GLU cc_start: 0.8573 (tm-30) cc_final: 0.7962 (tp30) REVERT: A 160 LEU cc_start: 0.8595 (tt) cc_final: 0.8233 (mp) REVERT: A 214 THR cc_start: 0.8521 (t) cc_final: 0.8250 (t) REVERT: B 20 TRP cc_start: 0.8379 (t-100) cc_final: 0.8151 (t60) REVERT: B 110 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8313 (tp30) REVERT: B 197 MET cc_start: 0.6780 (tpp) cc_final: 0.6515 (tpp) REVERT: B 377 MET cc_start: 0.8795 (mmm) cc_final: 0.8344 (mpp) REVERT: B 465 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8457 (tt) REVERT: C 92 PHE cc_start: 0.8349 (m-80) cc_final: 0.7970 (m-80) REVERT: C 95 SER cc_start: 0.9368 (p) cc_final: 0.9104 (p) REVERT: C 128 TYR cc_start: 0.8483 (t80) cc_final: 0.8194 (t80) REVERT: C 198 ASN cc_start: 0.8633 (t0) cc_final: 0.8253 (t0) REVERT: C 214 THR cc_start: 0.8503 (p) cc_final: 0.8217 (t) REVERT: C 239 MET cc_start: 0.8258 (tpp) cc_final: 0.6215 (tpp) REVERT: C 242 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7516 (pp20) REVERT: C 382 MET cc_start: 0.8714 (tpt) cc_final: 0.8491 (tpt) REVERT: D 29 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8392 (mpp80) REVERT: D 95 SER cc_start: 0.9256 (OUTLIER) cc_final: 0.8907 (p) REVERT: D 105 ASN cc_start: 0.8487 (m-40) cc_final: 0.8094 (m110) REVERT: D 160 LEU cc_start: 0.8617 (tt) cc_final: 0.8215 (mp) REVERT: D 197 MET cc_start: 0.6813 (tpp) cc_final: 0.6581 (tpp) REVERT: D 232 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7434 (tm-30) REVERT: D 352 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8743 (t) REVERT: D 426 GLN cc_start: 0.8385 (tp-100) cc_final: 0.8032 (tp-100) REVERT: D 433 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8277 (tm-30) outliers start: 40 outliers final: 24 residues processed: 293 average time/residue: 0.1846 time to fit residues: 82.0602 Evaluate side-chains 259 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 230 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL 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 336 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 242 GLU 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 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 352 THR Chi-restraints excluded: chain D residue 385 PHE 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 56 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 407 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12252 Z= 0.185 Angle : 0.652 9.529 16612 Z= 0.325 Chirality : 0.039 0.169 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.432 13.929 1624 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.91 % Allowed : 25.52 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.22), residues: 1476 helix: 2.83 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -1.24 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 20 HIS 0.002 0.000 HIS A 33 PHE 0.012 0.001 PHE C 92 TYR 0.026 0.002 TYR D 99 ARG 0.003 0.000 ARG B 37 *********************** 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 298 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 259 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8515 (tp40) REVERT: A 95 SER cc_start: 0.9320 (p) cc_final: 0.9086 (p) REVERT: A 160 LEU cc_start: 0.8580 (tt) cc_final: 0.8194 (mp) REVERT: A 214 THR cc_start: 0.8506 (t) cc_final: 0.8223 (t) REVERT: A 232 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 20 TRP cc_start: 0.8429 (t-100) cc_final: 0.8221 (t-100) REVERT: B 110 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 197 MET cc_start: 0.6891 (tpp) cc_final: 0.6599 (tpp) REVERT: B 214 THR cc_start: 0.8576 (t) cc_final: 0.8347 (t) REVERT: B 233 HIS cc_start: 0.8301 (t-90) cc_final: 0.7921 (t-90) REVERT: B 377 MET cc_start: 0.8796 (mmm) cc_final: 0.8335 (mpp) REVERT: B 465 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8477 (tt) REVERT: C 95 SER cc_start: 0.9388 (p) cc_final: 0.9130 (p) REVERT: C 128 TYR cc_start: 0.8467 (t80) cc_final: 0.8161 (t80) REVERT: C 130 MET cc_start: 0.8752 (mmm) cc_final: 0.8482 (mpp) REVERT: C 198 ASN cc_start: 0.8584 (t0) cc_final: 0.8283 (t0) REVERT: C 205 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7793 (tm-30) REVERT: C 214 THR cc_start: 0.8441 (p) cc_final: 0.8144 (t) REVERT: C 239 MET cc_start: 0.8294 (tpp) cc_final: 0.6813 (tpp) REVERT: C 242 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7601 (pp20) REVERT: D 29 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8435 (mpp80) REVERT: D 95 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.8965 (p) REVERT: D 105 ASN cc_start: 0.8450 (m-40) cc_final: 0.8040 (m110) REVERT: D 160 LEU cc_start: 0.8660 (tt) cc_final: 0.8234 (mp) REVERT: D 197 MET cc_start: 0.7141 (tpp) cc_final: 0.6771 (tpp) REVERT: D 232 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7452 (tm-30) REVERT: D 352 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8830 (t) REVERT: D 377 MET cc_start: 0.8534 (mmt) cc_final: 0.8023 (mpp) REVERT: D 426 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8071 (tp-100) REVERT: D 433 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8252 (tm-30) outliers start: 39 outliers final: 22 residues processed: 289 average time/residue: 0.1817 time to fit residues: 81.2961 Evaluate side-chains 259 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 232 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 59 ILE 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 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12252 Z= 0.203 Angle : 0.686 9.358 16612 Z= 0.336 Chirality : 0.039 0.168 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.422 13.741 1624 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.06 % Allowed : 25.90 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.22), residues: 1476 helix: 2.82 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -1.19 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C 20 HIS 0.002 0.000 HIS D 407 PHE 0.009 0.001 PHE C 113 TYR 0.030 0.002 TYR A 99 ARG 0.002 0.000 ARG B 37 *********************** 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 294 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 253 time to evaluate : 1.502 Fit side-chains REVERT: A 94 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8489 (tp40) REVERT: A 95 SER cc_start: 0.9317 (p) cc_final: 0.9086 (p) REVERT: A 110 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8408 (tm-30) REVERT: A 160 LEU cc_start: 0.8549 (tt) cc_final: 0.8137 (mp) REVERT: A 214 THR cc_start: 0.8530 (t) cc_final: 0.8256 (t) REVERT: A 232 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 382 MET cc_start: 0.8485 (tpp) cc_final: 0.8199 (tpt) REVERT: B 110 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8408 (tm-30) REVERT: B 118 GLU cc_start: 0.8004 (pm20) cc_final: 0.7764 (pm20) REVERT: B 197 MET cc_start: 0.6823 (tpp) cc_final: 0.6530 (tpp) REVERT: B 465 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8453 (tt) REVERT: C 95 SER cc_start: 0.9383 (p) cc_final: 0.9099 (p) REVERT: C 128 TYR cc_start: 0.8471 (t80) cc_final: 0.8150 (t80) REVERT: C 198 ASN cc_start: 0.8652 (t0) cc_final: 0.8341 (t0) REVERT: C 214 THR cc_start: 0.8438 (p) cc_final: 0.8151 (t) REVERT: C 239 MET cc_start: 0.8329 (tpp) cc_final: 0.6331 (tpp) REVERT: C 242 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7526 (pp20) REVERT: C 433 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8538 (tp-100) REVERT: D 95 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8940 (p) REVERT: D 105 ASN cc_start: 0.8419 (m-40) cc_final: 0.8034 (m110) REVERT: D 160 LEU cc_start: 0.8546 (tt) cc_final: 0.8141 (mp) REVERT: D 197 MET cc_start: 0.7150 (tpp) cc_final: 0.6804 (tpp) REVERT: D 232 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7471 (tm-30) REVERT: D 336 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7977 (pp20) REVERT: D 352 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8825 (t) REVERT: D 377 MET cc_start: 0.8535 (mmt) cc_final: 0.8016 (mpp) REVERT: D 426 GLN cc_start: 0.8459 (tp-100) cc_final: 0.8115 (tp-100) REVERT: D 433 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8196 (tm-30) outliers start: 41 outliers final: 27 residues processed: 286 average time/residue: 0.1878 time to fit residues: 82.6774 Evaluate side-chains 266 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 235 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 242 GLU 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 D residue 59 ILE Chi-restraints excluded: chain D residue 95 SER 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 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL 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 85 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 0.0170 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12252 Z= 0.196 Angle : 0.695 11.512 16612 Z= 0.339 Chirality : 0.039 0.164 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.400 14.858 1624 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.31 % Allowed : 26.72 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.22), residues: 1476 helix: 2.88 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 20 HIS 0.005 0.000 HIS B 233 PHE 0.012 0.001 PHE A 183 TYR 0.027 0.002 TYR D 99 ARG 0.003 0.000 ARG A 182 ********************** 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 284 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 253 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8387 (tp40) REVERT: A 95 SER cc_start: 0.9315 (p) cc_final: 0.9074 (p) REVERT: A 110 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 160 LEU cc_start: 0.8562 (tt) cc_final: 0.8147 (mp) REVERT: A 214 THR cc_start: 0.8500 (t) cc_final: 0.8227 (t) REVERT: A 232 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 110 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 197 MET cc_start: 0.6793 (tpp) cc_final: 0.6516 (tpp) REVERT: B 465 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8470 (tt) REVERT: C 95 SER cc_start: 0.9382 (p) cc_final: 0.9093 (p) REVERT: C 198 ASN cc_start: 0.8597 (t0) cc_final: 0.8327 (t0) REVERT: C 214 THR cc_start: 0.8434 (p) cc_final: 0.8146 (t) REVERT: C 239 MET cc_start: 0.8350 (tpp) cc_final: 0.6354 (tpp) REVERT: C 242 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: D 95 SER cc_start: 0.9267 (OUTLIER) cc_final: 0.8928 (p) REVERT: D 105 ASN cc_start: 0.8526 (m-40) cc_final: 0.8115 (m110) REVERT: D 160 LEU cc_start: 0.8540 (tt) cc_final: 0.8143 (mp) REVERT: D 197 MET cc_start: 0.7087 (tpp) cc_final: 0.6761 (tpp) REVERT: D 214 THR cc_start: 0.8553 (t) cc_final: 0.8301 (t) REVERT: D 232 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7425 (tm-30) REVERT: D 352 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8827 (t) REVERT: D 377 MET cc_start: 0.8567 (mmt) cc_final: 0.8053 (mpp) REVERT: D 426 GLN cc_start: 0.8491 (tp-100) cc_final: 0.8144 (tp-100) REVERT: D 433 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8241 (tm-30) outliers start: 31 outliers final: 25 residues processed: 279 average time/residue: 0.1785 time to fit residues: 77.5028 Evaluate side-chains 273 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 244 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 242 GLU 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 D residue 95 SER 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 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL 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 35 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 0.0470 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.105188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086941 restraints weight = 31744.891| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.48 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12252 Z= 0.180 Angle : 0.681 8.909 16612 Z= 0.332 Chirality : 0.039 0.161 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.394 14.828 1624 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.61 % Allowed : 26.87 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.22), residues: 1476 helix: 2.93 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -1.13 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 20 HIS 0.004 0.001 HIS B 233 PHE 0.008 0.001 PHE A 183 TYR 0.022 0.001 TYR D 99 ARG 0.002 0.000 ARG B 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2501.08 seconds wall clock time: 46 minutes 34.56 seconds (2794.56 seconds total)