Starting phenix.real_space_refine on Wed May 14 16:27:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lic_23372/05_2025/7lic_23372.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lic_23372/05_2025/7lic_23372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lic_23372/05_2025/7lic_23372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lic_23372/05_2025/7lic_23372.map" model { file = "/net/cci-nas-00/data/ceres_data/7lic_23372/05_2025/7lic_23372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lic_23372/05_2025/7lic_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-5687/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: 6.27, per 1000 atoms: 0.52 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 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: 1.01 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: 3.46 Time building geometry restraints manager: 3.48 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.010 Normalize map: mean=0, sd=1: 1.870 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 27.460 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.350 ------------------------------------------------------------------------------- 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= 0.219 Angle : 0.808 7.888 16612 Z= 0.482 Chirality : 0.045 0.185 1992 Planarity : 0.007 0.057 1988 Dihedral : 15.151 87.752 4300 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.27 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 Details of bonding type rmsd hydrogen bonds : bond 0.13588 ( 972) hydrogen bonds : angle 5.13909 ( 2892) covalent geometry : bond 0.00394 (12252) covalent geometry : angle 0.80812 (16612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 406 time to evaluate : 1.226 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: 0.2217 time to fit residues: 132.7794 Evaluate side-chains 233 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 229 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.104347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086280 restraints weight = 30290.946| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.42 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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= 0.153 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 Details of bonding type rmsd hydrogen bonds : bond 0.05691 ( 972) hydrogen bonds : angle 3.76318 ( 2892) covalent geometry : bond 0.00322 (12252) covalent geometry : angle 0.62025 (16612) *********************** 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 to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8946 (t0) cc_final: 0.8720 (t0) REVERT: A 110 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8392 (tp30) REVERT: A 158 TRP cc_start: 0.8460 (t-100) cc_final: 0.7381 (m-10) REVERT: A 197 MET cc_start: 0.5964 (tpp) cc_final: 0.5751 (tpp) REVERT: A 205 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8005 (tm-30) REVERT: A 233 HIS cc_start: 0.8861 (t-90) cc_final: 0.8473 (t70) REVERT: A 377 MET cc_start: 0.8620 (mpp) cc_final: 0.8226 (mpp) REVERT: A 419 ASP cc_start: 0.8783 (p0) cc_final: 0.8575 (p0) REVERT: B 84 ASN cc_start: 0.8905 (t0) cc_final: 0.8703 (t0) REVERT: B 110 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8428 (tp30) REVERT: B 157 MET cc_start: 0.8528 (tpt) cc_final: 0.8281 (ttm) REVERT: B 205 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 233 HIS cc_start: 0.8878 (t70) cc_final: 0.8437 (t70) REVERT: B 379 LEU cc_start: 0.7387 (tp) cc_final: 0.7147 (tp) REVERT: B 450 PHE cc_start: 0.8381 (t80) cc_final: 0.8133 (t80) REVERT: C 54 TYR cc_start: 0.7832 (t80) cc_final: 0.7570 (t80) REVERT: C 84 ASN cc_start: 0.8879 (t0) cc_final: 0.8656 (t0) REVERT: C 128 TYR cc_start: 0.8599 (t80) cc_final: 0.8022 (t80) REVERT: C 158 TRP cc_start: 0.8560 (t-100) cc_final: 0.7863 (m100) REVERT: C 198 ASN cc_start: 0.7944 (t0) cc_final: 0.7579 (t0) REVERT: C 205 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7810 (tm-30) REVERT: C 214 THR cc_start: 0.8447 (p) cc_final: 0.8139 (t) REVERT: C 222 MET cc_start: 0.8563 (tmm) cc_final: 0.8284 (tmm) REVERT: C 239 MET cc_start: 0.8583 (tpp) cc_final: 0.8157 (tpp) REVERT: C 352 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8298 (t) REVERT: D 84 ASN cc_start: 0.8847 (t0) cc_final: 0.8556 (t0) REVERT: D 110 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8347 (tp30) REVERT: D 158 TRP cc_start: 0.8444 (t-100) cc_final: 0.7471 (m-10) REVERT: D 205 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7967 (tm-30) REVERT: D 214 THR cc_start: 0.8445 (m) cc_final: 0.8172 (t) REVERT: D 377 MET cc_start: 0.8600 (mpp) cc_final: 0.8281 (mpp) outliers start: 33 outliers final: 13 residues processed: 303 average time/residue: 0.1915 time to fit residues: 88.3547 Evaluate side-chains 248 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain 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 352 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 415 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.0020 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 0.0670 overall best weight: 0.5526 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.103648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.084838 restraints weight = 31859.100| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.41 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12252 Z= 0.134 Angle : 0.593 7.474 16612 Z= 0.303 Chirality : 0.038 0.160 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.710 15.597 1624 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.39 % Allowed : 18.13 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.22), residues: 1476 helix: 2.31 (0.15), residues: 1208 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 20 HIS 0.003 0.001 HIS B 233 PHE 0.009 0.001 PHE A 450 TYR 0.019 0.001 TYR C 204 ARG 0.008 0.000 ARG D 431 Details of bonding type rmsd hydrogen bonds : bond 0.04939 ( 972) hydrogen bonds : angle 3.55096 ( 2892) covalent geometry : bond 0.00281 (12252) covalent geometry : angle 0.59308 (16612) *********************** 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 315 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8309 (tp30) REVERT: A 197 MET cc_start: 0.6440 (tpp) cc_final: 0.6158 (tpp) REVERT: A 205 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7901 (tm-30) REVERT: A 214 THR cc_start: 0.8413 (t) cc_final: 0.8150 (t) REVERT: A 233 HIS cc_start: 0.8709 (t-90) cc_final: 0.8398 (t70) REVERT: A 239 MET cc_start: 0.8753 (tpp) cc_final: 0.8424 (tpp) REVERT: A 352 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8458 (t) REVERT: A 377 MET cc_start: 0.8569 (mpp) cc_final: 0.8228 (mpp) REVERT: A 379 LEU cc_start: 0.7794 (tp) cc_final: 0.7589 (tp) REVERT: A 419 ASP cc_start: 0.8663 (p0) cc_final: 0.8439 (p0) REVERT: B 84 ASN cc_start: 0.8894 (t0) cc_final: 0.8623 (t0) REVERT: B 110 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8479 (tp30) REVERT: B 141 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8337 (pttp) REVERT: B 158 TRP cc_start: 0.8217 (t-100) cc_final: 0.7541 (m-10) REVERT: B 197 MET cc_start: 0.6382 (tpp) cc_final: 0.6159 (tpp) REVERT: B 205 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 214 THR cc_start: 0.8565 (m) cc_final: 0.8305 (t) REVERT: B 352 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8321 (t) REVERT: B 377 MET cc_start: 0.8885 (mmm) cc_final: 0.8403 (mpp) REVERT: C 54 TYR cc_start: 0.8042 (t80) cc_final: 0.7815 (t80) REVERT: C 95 SER cc_start: 0.9446 (p) cc_final: 0.9147 (p) REVERT: C 128 TYR cc_start: 0.8803 (t80) cc_final: 0.8294 (t80) REVERT: C 205 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7844 (tm-30) REVERT: C 214 THR cc_start: 0.8601 (p) cc_final: 0.8277 (t) REVERT: C 222 MET cc_start: 0.8694 (tmm) cc_final: 0.8406 (tmm) REVERT: C 239 MET cc_start: 0.8882 (tpp) cc_final: 0.6872 (tpp) REVERT: C 242 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7854 (pp20) REVERT: C 342 TYR cc_start: 0.7296 (m-80) cc_final: 0.6999 (m-10) REVERT: C 383 TYR cc_start: 0.8717 (t80) cc_final: 0.8329 (t80) REVERT: D 84 ASN cc_start: 0.8793 (t0) cc_final: 0.8566 (t0) REVERT: D 110 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8283 (tp30) REVERT: D 157 MET cc_start: 0.8346 (tpt) cc_final: 0.8008 (ttm) REVERT: D 158 TRP cc_start: 0.8380 (t-100) cc_final: 0.7552 (m-10) REVERT: D 197 MET cc_start: 0.5909 (tpp) cc_final: 0.5645 (tpp) REVERT: D 205 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7948 (tm-30) REVERT: D 214 THR cc_start: 0.8601 (m) cc_final: 0.8340 (t) REVERT: D 352 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8492 (t) REVERT: D 377 MET cc_start: 0.8605 (mpp) cc_final: 0.8271 (mpp) REVERT: D 379 LEU cc_start: 0.7694 (tp) cc_final: 0.7310 (tp) outliers start: 32 outliers final: 18 residues processed: 304 average time/residue: 0.1786 time to fit residues: 82.9128 Evaluate side-chains 269 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 B residue 109 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 59 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 69 optimal weight: 0.0020 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 0.0370 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.1670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS C 233 HIS D 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.101531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083280 restraints weight = 31490.381| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.30 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3473 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= 0.155 Angle : 0.610 9.475 16612 Z= 0.315 Chirality : 0.039 0.166 1992 Planarity : 0.004 0.043 1988 Dihedral : 3.583 15.287 1624 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.43 % Allowed : 19.63 % Favored : 76.94 % 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: 2.78 (0.22), residues: 1476 helix: 2.47 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.23 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 20 HIS 0.005 0.001 HIS B 233 PHE 0.013 0.001 PHE C 183 TYR 0.026 0.002 TYR B 99 ARG 0.004 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.05103 ( 972) hydrogen bonds : angle 3.59362 ( 2892) covalent geometry : bond 0.00339 (12252) covalent geometry : angle 0.61050 (16612) *********************** 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 292 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 1.407 Fit side-chains REVERT: A 110 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8394 (tp30) REVERT: A 205 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 233 HIS cc_start: 0.8772 (t-90) cc_final: 0.8508 (t70) REVERT: A 352 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8574 (t) REVERT: A 377 MET cc_start: 0.8630 (mpp) cc_final: 0.8307 (mpp) REVERT: A 433 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8702 (tm-30) REVERT: B 84 ASN cc_start: 0.8919 (t0) cc_final: 0.8634 (t0) REVERT: B 95 SER cc_start: 0.9403 (p) cc_final: 0.9167 (p) REVERT: B 110 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8549 (tp30) REVERT: B 197 MET cc_start: 0.6408 (tpp) cc_final: 0.6144 (tpp) REVERT: B 205 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 220 ASP cc_start: 0.9328 (t70) cc_final: 0.9097 (t70) REVERT: B 377 MET cc_start: 0.8960 (mmm) cc_final: 0.8386 (mpp) REVERT: C 84 ASN cc_start: 0.8957 (t0) cc_final: 0.8755 (t0) REVERT: C 95 SER cc_start: 0.9429 (p) cc_final: 0.9181 (p) REVERT: C 157 MET cc_start: 0.7674 (tpt) cc_final: 0.7460 (ttp) REVERT: C 198 ASN cc_start: 0.8278 (t0) cc_final: 0.7788 (t0) REVERT: C 205 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 214 THR cc_start: 0.8490 (p) cc_final: 0.8167 (t) REVERT: C 222 MET cc_start: 0.8875 (tmm) cc_final: 0.8455 (tmm) REVERT: C 239 MET cc_start: 0.8922 (tpp) cc_final: 0.6951 (tpp) REVERT: C 242 GLU cc_start: 0.8542 (pp20) cc_final: 0.7837 (pp20) REVERT: C 342 TYR cc_start: 0.7321 (m-80) cc_final: 0.6938 (m-10) REVERT: C 352 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8564 (t) REVERT: D 84 ASN cc_start: 0.8927 (t0) cc_final: 0.8658 (t0) REVERT: D 105 ASN cc_start: 0.9047 (m-40) cc_final: 0.8743 (m110) REVERT: D 110 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8374 (tp30) REVERT: D 157 MET cc_start: 0.8480 (tpt) cc_final: 0.8032 (ttm) REVERT: D 197 MET cc_start: 0.6065 (tpp) cc_final: 0.5720 (tpp) REVERT: D 205 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7968 (tm-30) REVERT: D 352 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8577 (t) REVERT: D 377 MET cc_start: 0.8697 (mpp) cc_final: 0.8352 (mpp) REVERT: D 379 LEU cc_start: 0.7646 (tp) cc_final: 0.7325 (tp) REVERT: D 382 MET cc_start: 0.8670 (tpp) cc_final: 0.8463 (tpt) outliers start: 46 outliers final: 29 residues processed: 283 average time/residue: 0.1726 time to fit residues: 76.6320 Evaluate side-chains 264 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 466 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 420 HIS 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 352 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain 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 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 466 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 0.0870 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.097112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079152 restraints weight = 32755.589| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.30 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12252 Z= 0.206 Angle : 0.684 10.163 16612 Z= 0.349 Chirality : 0.041 0.176 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.677 14.617 1624 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.28 % Allowed : 22.39 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.77 (0.22), residues: 1476 helix: 2.44 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.08 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 20 HIS 0.003 0.001 HIS A 420 PHE 0.018 0.001 PHE C 183 TYR 0.024 0.002 TYR A 99 ARG 0.003 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.05734 ( 972) hydrogen bonds : angle 3.82083 ( 2892) covalent geometry : bond 0.00457 (12252) covalent geometry : angle 0.68361 (16612) *********************** 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 284 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 1.350 Fit side-chains REVERT: A 20 TRP cc_start: 0.8830 (t-100) cc_final: 0.8525 (t-100) REVERT: A 110 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8410 (tp30) REVERT: A 141 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8422 (mmtm) REVERT: A 205 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 233 HIS cc_start: 0.8858 (t-90) cc_final: 0.8613 (t70) REVERT: A 352 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8658 (t) REVERT: A 377 MET cc_start: 0.8697 (mpp) cc_final: 0.8327 (mpp) REVERT: A 433 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8653 (tm-30) REVERT: B 95 SER cc_start: 0.9427 (p) cc_final: 0.9135 (p) REVERT: B 110 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8491 (tp30) REVERT: B 197 MET cc_start: 0.6421 (tpp) cc_final: 0.6095 (tpp) REVERT: B 205 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8129 (tm-30) REVERT: B 220 ASP cc_start: 0.9364 (t70) cc_final: 0.9159 (t70) REVERT: C 83 LEU cc_start: 0.8739 (mm) cc_final: 0.8522 (mm) REVERT: C 84 ASN cc_start: 0.8867 (t0) cc_final: 0.8456 (t0) REVERT: C 95 SER cc_start: 0.9419 (p) cc_final: 0.9136 (p) REVERT: C 105 ASN cc_start: 0.8884 (m-40) cc_final: 0.8662 (m-40) REVERT: C 198 ASN cc_start: 0.8339 (t0) cc_final: 0.7846 (t0) REVERT: C 205 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7678 (tm-30) REVERT: C 214 THR cc_start: 0.8527 (p) cc_final: 0.8181 (t) REVERT: C 222 MET cc_start: 0.8943 (tmm) cc_final: 0.8581 (tmm) REVERT: C 239 MET cc_start: 0.8933 (tpp) cc_final: 0.8641 (tpp) REVERT: C 342 TYR cc_start: 0.7570 (m-80) cc_final: 0.6856 (m-10) REVERT: C 352 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8623 (t) REVERT: C 377 MET cc_start: 0.8464 (mmt) cc_final: 0.8238 (mmt) REVERT: D 83 LEU cc_start: 0.8889 (mm) cc_final: 0.8684 (mm) REVERT: D 105 ASN cc_start: 0.9136 (m-40) cc_final: 0.8796 (m-40) REVERT: D 110 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8497 (tp30) REVERT: D 157 MET cc_start: 0.8483 (tpt) cc_final: 0.8020 (ttm) REVERT: D 205 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8053 (tm-30) REVERT: D 220 ASP cc_start: 0.9272 (t70) cc_final: 0.9018 (t70) REVERT: D 352 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8629 (t) REVERT: D 377 MET cc_start: 0.8731 (mpp) cc_final: 0.8371 (mpp) REVERT: D 433 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8501 (tm-30) outliers start: 44 outliers final: 29 residues processed: 276 average time/residue: 0.1777 time to fit residues: 76.3698 Evaluate side-chains 253 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 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 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 352 THR Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 21 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 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.098693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.080759 restraints weight = 33198.229| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 4.35 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12252 Z= 0.152 Angle : 0.637 9.954 16612 Z= 0.319 Chirality : 0.039 0.181 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.549 14.772 1624 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.36 % Allowed : 23.58 % Favored : 73.06 % 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: 2.96 (0.22), residues: 1476 helix: 2.58 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.07 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 20 HIS 0.002 0.000 HIS D 407 PHE 0.009 0.001 PHE A 92 TYR 0.024 0.002 TYR A 99 ARG 0.002 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 972) hydrogen bonds : angle 3.61635 ( 2892) covalent geometry : bond 0.00330 (12252) covalent geometry : angle 0.63661 (16612) *********************** 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 292 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.273 Fit side-chains REVERT: A 105 ASN cc_start: 0.8697 (m110) cc_final: 0.8475 (m-40) REVERT: A 110 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8410 (tp30) REVERT: A 141 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8397 (pttp) REVERT: A 197 MET cc_start: 0.6825 (tpp) cc_final: 0.6615 (tpp) REVERT: A 205 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 352 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8622 (t) REVERT: A 433 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8619 (tm-30) REVERT: B 83 LEU cc_start: 0.8982 (mm) cc_final: 0.8757 (mm) REVERT: B 84 ASN cc_start: 0.8973 (t0) cc_final: 0.8558 (t0) REVERT: B 110 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8499 (tp30) REVERT: B 158 TRP cc_start: 0.8317 (t-100) cc_final: 0.7915 (t60) REVERT: B 197 MET cc_start: 0.6392 (tpp) cc_final: 0.6060 (tpp) REVERT: B 205 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 239 MET cc_start: 0.8768 (tpp) cc_final: 0.8497 (tpp) REVERT: C 83 LEU cc_start: 0.8673 (mm) cc_final: 0.8430 (mm) REVERT: C 95 SER cc_start: 0.9458 (p) cc_final: 0.9206 (p) REVERT: C 105 ASN cc_start: 0.8866 (m-40) cc_final: 0.8574 (m-40) REVERT: C 198 ASN cc_start: 0.8461 (t0) cc_final: 0.7961 (t0) REVERT: C 205 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 214 THR cc_start: 0.8517 (p) cc_final: 0.8192 (t) REVERT: C 222 MET cc_start: 0.8882 (tmm) cc_final: 0.8610 (tmm) REVERT: C 239 MET cc_start: 0.8874 (tpp) cc_final: 0.6978 (tpp) REVERT: C 242 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7804 (pp20) REVERT: C 352 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8606 (t) REVERT: C 377 MET cc_start: 0.8465 (mmt) cc_final: 0.8265 (mmt) REVERT: D 105 ASN cc_start: 0.8999 (m-40) cc_final: 0.8693 (m-40) REVERT: D 110 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8450 (tp30) REVERT: D 157 MET cc_start: 0.8530 (tpt) cc_final: 0.8022 (ttm) REVERT: D 197 MET cc_start: 0.6334 (tpp) cc_final: 0.5896 (tpp) REVERT: D 205 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7997 (tm-30) REVERT: D 239 MET cc_start: 0.8807 (tpp) cc_final: 0.8589 (tpp) REVERT: D 352 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8619 (t) REVERT: D 377 MET cc_start: 0.8735 (mpp) cc_final: 0.8381 (mpp) REVERT: D 433 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8544 (tm-30) outliers start: 45 outliers final: 26 residues processed: 285 average time/residue: 0.1742 time to fit residues: 77.0891 Evaluate side-chains 250 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 71 ILE 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 420 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 388 ILE 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 147 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 446 VAL Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7107 > 50: distance: 39 - 56: 36.841 distance: 43 - 62: 37.060 distance: 48 - 73: 33.670 distance: 51 - 56: 34.648 distance: 52 - 81: 27.089 distance: 56 - 57: 47.113 distance: 57 - 58: 40.443 distance: 57 - 60: 16.623 distance: 58 - 59: 36.539 distance: 58 - 62: 34.308 distance: 59 - 89: 42.491 distance: 60 - 61: 40.267 distance: 62 - 63: 39.116 distance: 63 - 64: 39.081 distance: 63 - 66: 39.211 distance: 64 - 73: 39.498 distance: 66 - 67: 56.783 distance: 67 - 68: 39.902 distance: 67 - 69: 41.753 distance: 68 - 70: 57.108 distance: 69 - 71: 37.863 distance: 70 - 72: 15.770 distance: 71 - 72: 30.741 distance: 73 - 74: 38.232 distance: 74 - 75: 37.493 distance: 74 - 77: 39.385 distance: 75 - 76: 55.893 distance: 75 - 81: 19.588 distance: 77 - 78: 56.384 distance: 77 - 79: 55.654 distance: 78 - 80: 46.075 distance: 82 - 83: 29.742 distance: 82 - 85: 16.813 distance: 83 - 84: 42.463 distance: 83 - 89: 4.296 distance: 85 - 86: 8.527 distance: 85 - 87: 40.617 distance: 89 - 90: 30.110 distance: 90 - 91: 43.194 distance: 90 - 93: 38.793 distance: 91 - 92: 16.403 distance: 91 - 97: 58.141 distance: 93 - 94: 70.026 distance: 94 - 95: 56.195 distance: 94 - 96: 38.996 distance: 98 - 99: 21.641 distance: 98 - 101: 40.743 distance: 99 - 100: 39.011 distance: 99 - 103: 34.129 distance: 103 - 104: 54.088 distance: 104 - 105: 57.217 distance: 104 - 107: 12.896 distance: 105 - 106: 44.697 distance: 105 - 114: 28.598 distance: 106 - 140: 24.094 distance: 107 - 108: 47.856 distance: 109 - 110: 10.883 distance: 110 - 111: 22.934 distance: 111 - 112: 53.913 distance: 111 - 113: 35.719 distance: 114 - 115: 23.862 distance: 115 - 116: 21.189 distance: 115 - 118: 52.053 distance: 116 - 117: 47.467 distance: 116 - 123: 41.303 distance: 117 - 147: 35.585 distance: 118 - 119: 39.215 distance: 119 - 120: 63.196 distance: 120 - 121: 24.100 distance: 121 - 122: 58.152 distance: 124 - 125: 57.445 distance: 124 - 127: 40.477 distance: 125 - 126: 41.094 distance: 125 - 131: 38.850 distance: 126 - 155: 32.922 distance: 128 - 130: 5.374 distance: 131 - 132: 27.957 distance: 132 - 133: 19.935 distance: 132 - 135: 19.794 distance: 133 - 134: 43.983 distance: 133 - 140: 31.532 distance: 134 - 164: 32.974 distance: 135 - 136: 44.187 distance: 136 - 137: 52.854