Starting phenix.real_space_refine on Wed Sep 17 21:41:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zw8_60519/09_2025/8zw8_60519.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zw8_60519/09_2025/8zw8_60519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zw8_60519/09_2025/8zw8_60519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zw8_60519/09_2025/8zw8_60519.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zw8_60519/09_2025/8zw8_60519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zw8_60519/09_2025/8zw8_60519.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.066 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 48 5.16 5 C 7845 2.51 5 N 1794 2.21 5 O 1965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11652 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3884 Classifications: {'peptide': 497} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 478} Chain: "B" Number of atoms: 3884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3884 Classifications: {'peptide': 497} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 477} Chain: "C" Number of atoms: 3884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3884 Classifications: {'peptide': 497} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 477} Time building chain proxies: 3.07, per 1000 atoms: 0.26 Number of scatterers: 11652 At special positions: 0 Unit cell: (111.3, 117.66, 83.74, 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 48 16.00 O 1965 8.00 N 1794 7.00 C 7845 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: 0.71 Conformation dependent library (CDL) restraints added in 556.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 86.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 14 through 35 removed outlier: 3.997A pdb=" N THR A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 74 Proline residue: A 44 - end of helix removed outlier: 5.712A pdb=" N TRP A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 106 through 123 removed outlier: 3.816A pdb=" N MET A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE A 114 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.513A pdb=" N PHE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 148 through 167 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 190 through 226 removed outlier: 4.036A pdb=" N ILE A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 251 Processing helix chain 'A' and resid 257 through 279 Processing helix chain 'A' and resid 281 through 298 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.557A pdb=" N VAL A 333 " --> pdb=" O TRP A 329 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 378 removed outlier: 3.599A pdb=" N VAL A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Proline residue: A 357 - end of helix removed outlier: 3.514A pdb=" N LEU A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 404 through 437 removed outlier: 3.514A pdb=" N SER A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 464 removed outlier: 3.825A pdb=" N ARG A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 504 Proline residue: A 480 - end of helix Processing helix chain 'B' and resid 14 through 34 removed outlier: 3.682A pdb=" N THR B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 74 removed outlier: 3.637A pdb=" N VAL B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) Proline residue: B 44 - end of helix removed outlier: 5.720A pdb=" N TRP B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 92 through 103 removed outlier: 3.703A pdb=" N MET B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 5.616A pdb=" N ILE B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 117 - end of helix removed outlier: 3.662A pdb=" N PHE B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 184 through 188 removed outlier: 3.551A pdb=" N GLY B 188 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 226 removed outlier: 4.113A pdb=" N ILE B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 251 Processing helix chain 'B' and resid 255 through 279 Processing helix chain 'B' and resid 281 through 298 Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.597A pdb=" N THR B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 340 Proline residue: B 331 - end of helix removed outlier: 3.667A pdb=" N PHE B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 355 Processing helix chain 'B' and resid 355 through 378 removed outlier: 3.958A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 removed outlier: 3.534A pdb=" N ALA B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 399 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 404 through 437 removed outlier: 4.065A pdb=" N LEU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 464 removed outlier: 3.654A pdb=" N ARG B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 504 Proline residue: B 480 - end of helix removed outlier: 3.753A pdb=" N GLN B 493 " --> pdb=" O CYS B 489 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 494 " --> pdb=" O TYR B 490 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 35 removed outlier: 3.906A pdb=" N THR C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 74 Proline residue: C 44 - end of helix removed outlier: 5.729A pdb=" N TRP C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.704A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 removed outlier: 3.782A pdb=" N MET C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 148 through 167 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 190 through 226 removed outlier: 4.054A pdb=" N ILE C 194 " --> pdb=" O TRP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 249 Processing helix chain 'C' and resid 257 through 279 Processing helix chain 'C' and resid 281 through 298 Processing helix chain 'C' and resid 298 through 304 removed outlier: 3.504A pdb=" N THR C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.501A pdb=" N VAL C 317 " --> pdb=" O TRP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 329 through 340 removed outlier: 3.732A pdb=" N PHE C 336 " --> pdb=" O PHE C 332 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 355 Processing helix chain 'C' and resid 355 through 378 removed outlier: 3.952A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 Processing helix chain 'C' and resid 393 through 399 Processing helix chain 'C' and resid 400 through 402 No H-bonds generated for 'chain 'C' and resid 400 through 402' Processing helix chain 'C' and resid 404 through 437 removed outlier: 3.544A pdb=" N SER C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 464 removed outlier: 3.774A pdb=" N ARG C 447 " --> pdb=" O PRO C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 504 Proline residue: C 480 - end of helix removed outlier: 3.712A pdb=" N GLN C 493 " --> pdb=" O CYS C 489 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 494 " --> pdb=" O TYR C 490 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.05 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: 3407 1.34 - 1.46: 3187 1.46 - 1.58: 5325 1.58 - 1.70: 0 1.70 - 1.81: 90 Bond restraints: 12009 Sorted by residual: bond pdb=" CA VAL A 381 " pdb=" CB VAL A 381 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.31e-02 5.83e+03 1.44e+00 bond pdb=" C VAL C 356 " pdb=" N PRO C 357 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.23e-02 6.61e+03 1.38e+00 bond pdb=" CA LEU C 11 " pdb=" CB LEU C 11 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.35e-02 5.49e+03 1.16e+00 bond pdb=" CB THR C 142 " pdb=" CG2 THR C 142 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.13e+00 bond pdb=" CB VAL B 474 " pdb=" CG1 VAL B 474 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.95e-01 ... (remaining 12004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 16091 1.84 - 3.68: 238 3.68 - 5.52: 37 5.52 - 7.36: 10 7.36 - 9.20: 7 Bond angle restraints: 16383 Sorted by residual: angle pdb=" C LEU B 253 " pdb=" N ASP B 254 " pdb=" CA ASP B 254 " ideal model delta sigma weight residual 121.70 129.77 -8.07 1.80e+00 3.09e-01 2.01e+01 angle pdb=" C GLY B 104 " pdb=" N MET B 105 " pdb=" CA MET B 105 " ideal model delta sigma weight residual 121.70 129.59 -7.89 1.80e+00 3.09e-01 1.92e+01 angle pdb=" N VAL B 317 " pdb=" CA VAL B 317 " pdb=" C VAL B 317 " ideal model delta sigma weight residual 113.53 110.21 3.32 9.80e-01 1.04e+00 1.15e+01 angle pdb=" N TRP B 190 " pdb=" CA TRP B 190 " pdb=" C TRP B 190 " ideal model delta sigma weight residual 113.43 109.16 4.27 1.26e+00 6.30e-01 1.15e+01 angle pdb=" N SER B 251 " pdb=" CA SER B 251 " pdb=" C SER B 251 " ideal model delta sigma weight residual 112.68 109.08 3.60 1.33e+00 5.65e-01 7.32e+00 ... (remaining 16378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5725 17.53 - 35.07: 773 35.07 - 52.60: 172 52.60 - 70.13: 28 70.13 - 87.67: 7 Dihedral angle restraints: 6705 sinusoidal: 2472 harmonic: 4233 Sorted by residual: dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N PHE A 35 " pdb=" CA PHE A 35 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA TRP B 323 " pdb=" CB TRP B 323 " pdb=" CG TRP B 323 " pdb=" CD1 TRP B 323 " ideal model delta sinusoidal sigma weight residual 90.00 161.03 -71.03 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA TRP A 323 " pdb=" CB TRP A 323 " pdb=" CG TRP A 323 " pdb=" CD1 TRP A 323 " ideal model delta sinusoidal sigma weight residual 90.00 160.81 -70.81 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 6702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1321 0.040 - 0.080: 463 0.080 - 0.120: 98 0.120 - 0.160: 7 0.160 - 0.200: 1 Chirality restraints: 1890 Sorted by residual: chirality pdb=" CB ILE C 456 " pdb=" CA ILE C 456 " pdb=" CG1 ILE C 456 " pdb=" CG2 ILE C 456 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB ILE A 456 " pdb=" CA ILE A 456 " pdb=" CG1 ILE A 456 " pdb=" CG2 ILE A 456 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CB ILE B 456 " pdb=" CA ILE B 456 " pdb=" CG1 ILE B 456 " pdb=" CG2 ILE B 456 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1887 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 35 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO B 36 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 329 " -0.015 2.00e-02 2.50e+03 1.54e-02 5.95e+00 pdb=" CG TRP B 329 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 329 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 329 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 329 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 329 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 329 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 329 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 329 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 43 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.71e+00 pdb=" N PRO A 44 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " -0.034 5.00e-02 4.00e+02 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 173 2.69 - 3.24: 11813 3.24 - 3.80: 19739 3.80 - 4.35: 24691 4.35 - 4.90: 43077 Nonbonded interactions: 99493 Sorted by model distance: nonbonded pdb=" OD2 ASP C 432 " pdb=" OG SER C 442 " model vdw 2.140 3.040 nonbonded pdb=" OD2 ASP B 432 " pdb=" OG SER B 442 " model vdw 2.188 3.040 nonbonded pdb=" OE1 GLN C 140 " pdb=" ND2 ASN C 298 " model vdw 2.195 3.120 nonbonded pdb=" O PHE B 299 " pdb=" OG SER B 303 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASN A 264 " pdb=" OG SER A 418 " model vdw 2.213 3.040 ... (remaining 99488 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.160 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.003 0.037 12009 Z= 0.141 Angle : 0.597 9.204 16383 Z= 0.329 Chirality : 0.040 0.200 1890 Planarity : 0.005 0.084 1974 Dihedral : 16.411 87.668 3993 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.65 % Allowed : 25.69 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.22), residues: 1485 helix: 1.51 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -0.48 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 175 TYR 0.005 0.001 TYR C 295 PHE 0.028 0.001 PHE C 417 TRP 0.041 0.001 TRP B 329 HIS 0.002 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00307 (12009) covalent geometry : angle 0.59744 (16383) hydrogen bonds : bond 0.13352 ( 909) hydrogen bonds : angle 5.59761 ( 2670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.417 Fit side-chains REVERT: A 232 MET cc_start: 0.7110 (tpp) cc_final: 0.6216 (ttm) REVERT: A 425 ASP cc_start: 0.8188 (t0) cc_final: 0.7782 (m-30) REVERT: B 18 PHE cc_start: 0.7605 (t80) cc_final: 0.7310 (t80) outliers start: 8 outliers final: 7 residues processed: 159 average time/residue: 0.0908 time to fit residues: 21.7852 Evaluate side-chains 157 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 426 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 47 GLN C 140 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 ASN C 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.144547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.101522 restraints weight = 12694.157| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.82 r_work: 0.3010 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12009 Z= 0.144 Angle : 0.553 8.532 16383 Z= 0.293 Chirality : 0.041 0.135 1890 Planarity : 0.004 0.041 1974 Dihedral : 4.668 41.810 1559 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.11 % Allowed : 25.04 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.22), residues: 1485 helix: 1.58 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.35 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 175 TYR 0.008 0.001 TYR B 322 PHE 0.028 0.001 PHE A 417 TRP 0.020 0.001 TRP B 329 HIS 0.003 0.001 HIS A 187 Details of bonding type rmsd covalent geometry : bond 0.00330 (12009) covalent geometry : angle 0.55325 (16383) hydrogen bonds : bond 0.04417 ( 909) hydrogen bonds : angle 4.64601 ( 2670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.364 Fit side-chains REVERT: A 22 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.7028 (mt) REVERT: A 175 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.6673 (ttm-80) REVERT: A 232 MET cc_start: 0.7366 (tpp) cc_final: 0.6432 (ttm) REVERT: A 425 ASP cc_start: 0.8431 (t0) cc_final: 0.8151 (m-30) REVERT: B 273 LEU cc_start: 0.8088 (tp) cc_final: 0.7558 (mt) REVERT: B 301 ASP cc_start: 0.8241 (t0) cc_final: 0.7802 (t0) REVERT: B 380 ASP cc_start: 0.8721 (t0) cc_final: 0.8502 (t0) REVERT: B 390 ASP cc_start: 0.7259 (p0) cc_final: 0.6933 (p0) REVERT: C 22 ILE cc_start: 0.7415 (mm) cc_final: 0.7170 (mt) REVERT: C 232 MET cc_start: 0.7834 (tpt) cc_final: 0.7169 (tpp) outliers start: 26 outliers final: 16 residues processed: 187 average time/residue: 0.0865 time to fit residues: 24.5336 Evaluate side-chains 174 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 33 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.152180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110198 restraints weight = 12864.915| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.88 r_work: 0.2991 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12009 Z= 0.187 Angle : 0.580 10.086 16383 Z= 0.304 Chirality : 0.043 0.142 1890 Planarity : 0.004 0.040 1974 Dihedral : 4.338 21.416 1550 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.93 % Allowed : 23.09 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.22), residues: 1485 helix: 1.49 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -0.42 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 175 TYR 0.011 0.001 TYR B 322 PHE 0.024 0.002 PHE C 122 TRP 0.025 0.001 TRP B 329 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00451 (12009) covalent geometry : angle 0.57964 (16383) hydrogen bonds : bond 0.04611 ( 909) hydrogen bonds : angle 4.63694 ( 2670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.268 Fit side-chains REVERT: A 22 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7264 (mt) REVERT: A 425 ASP cc_start: 0.8450 (t0) cc_final: 0.8176 (m-30) REVERT: B 273 LEU cc_start: 0.8137 (tp) cc_final: 0.7566 (mt) REVERT: B 301 ASP cc_start: 0.8229 (t0) cc_final: 0.7836 (t0) REVERT: B 380 ASP cc_start: 0.8714 (t0) cc_final: 0.8480 (t70) REVERT: C 232 MET cc_start: 0.7801 (tpt) cc_final: 0.7165 (tpp) outliers start: 36 outliers final: 31 residues processed: 185 average time/residue: 0.0862 time to fit residues: 23.9278 Evaluate side-chains 182 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 496 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.152548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.111289 restraints weight = 12779.587| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.74 r_work: 0.3054 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12009 Z= 0.145 Angle : 0.539 8.763 16383 Z= 0.284 Chirality : 0.041 0.134 1890 Planarity : 0.004 0.041 1974 Dihedral : 4.257 19.227 1550 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.01 % Allowed : 23.25 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.22), residues: 1485 helix: 1.59 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.52 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.006 0.001 TYR B 322 PHE 0.028 0.002 PHE A 417 TRP 0.020 0.001 TRP B 329 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00337 (12009) covalent geometry : angle 0.53899 (16383) hydrogen bonds : bond 0.04262 ( 909) hydrogen bonds : angle 4.52884 ( 2670) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.414 Fit side-chains REVERT: A 22 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7265 (mt) REVERT: A 175 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.6776 (ttm-80) REVERT: A 425 ASP cc_start: 0.8442 (t0) cc_final: 0.8155 (m-30) REVERT: A 496 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 273 LEU cc_start: 0.8128 (tp) cc_final: 0.7563 (mt) REVERT: B 301 ASP cc_start: 0.8205 (t0) cc_final: 0.7812 (t0) REVERT: B 380 ASP cc_start: 0.8688 (t0) cc_final: 0.8478 (t0) REVERT: B 383 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8139 (mtm) REVERT: B 390 ASP cc_start: 0.7347 (p0) cc_final: 0.6892 (p0) REVERT: C 144 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8732 (tp) REVERT: C 232 MET cc_start: 0.7791 (tpt) cc_final: 0.7172 (tpp) REVERT: C 285 MET cc_start: 0.8049 (mmm) cc_final: 0.7770 (mmm) outliers start: 37 outliers final: 30 residues processed: 177 average time/residue: 0.0933 time to fit residues: 24.9870 Evaluate side-chains 182 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 496 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 32 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115896 restraints weight = 12753.065| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.59 r_work: 0.2886 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12009 Z= 0.168 Angle : 0.555 9.473 16383 Z= 0.292 Chirality : 0.042 0.136 1890 Planarity : 0.004 0.040 1974 Dihedral : 4.282 20.326 1550 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.66 % Allowed : 22.93 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.21), residues: 1485 helix: 1.54 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.53 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.008 0.001 TYR B 322 PHE 0.023 0.002 PHE A 420 TRP 0.025 0.001 TRP B 329 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00400 (12009) covalent geometry : angle 0.55508 (16383) hydrogen bonds : bond 0.04386 ( 909) hydrogen bonds : angle 4.54928 ( 2670) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.365 Fit side-chains REVERT: A 22 ILE cc_start: 0.7105 (mm) cc_final: 0.6864 (mt) REVERT: A 116 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8587 (tt0) REVERT: A 425 ASP cc_start: 0.8338 (t0) cc_final: 0.8014 (m-30) REVERT: A 496 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7515 (mp) REVERT: B 273 LEU cc_start: 0.7856 (tp) cc_final: 0.7256 (mt) REVERT: B 301 ASP cc_start: 0.8260 (t0) cc_final: 0.7808 (t0) REVERT: B 380 ASP cc_start: 0.8511 (t0) cc_final: 0.8240 (t0) REVERT: B 383 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8076 (mtm) REVERT: C 144 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8550 (tp) REVERT: C 232 MET cc_start: 0.7751 (tpt) cc_final: 0.7111 (tpp) REVERT: C 285 MET cc_start: 0.8036 (mmm) cc_final: 0.7660 (mmm) outliers start: 45 outliers final: 37 residues processed: 187 average time/residue: 0.0897 time to fit residues: 25.2408 Evaluate side-chains 189 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 496 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.142509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099554 restraints weight = 12828.782| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.84 r_work: 0.3029 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12009 Z= 0.140 Angle : 0.532 8.608 16383 Z= 0.281 Chirality : 0.041 0.148 1890 Planarity : 0.004 0.040 1974 Dihedral : 4.208 18.640 1550 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.58 % Allowed : 22.93 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.22), residues: 1485 helix: 1.63 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.52 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 175 TYR 0.005 0.001 TYR B 295 PHE 0.029 0.001 PHE A 417 TRP 0.020 0.001 TRP B 329 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00323 (12009) covalent geometry : angle 0.53222 (16383) hydrogen bonds : bond 0.04189 ( 909) hydrogen bonds : angle 4.48138 ( 2670) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.405 Fit side-chains REVERT: A 22 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7152 (mt) REVERT: A 116 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8714 (tt0) REVERT: A 285 MET cc_start: 0.8371 (mmm) cc_final: 0.7991 (mmt) REVERT: A 425 ASP cc_start: 0.8487 (t0) cc_final: 0.8192 (m-30) REVERT: A 496 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7874 (mp) REVERT: B 273 LEU cc_start: 0.8101 (tp) cc_final: 0.7518 (mt) REVERT: B 301 ASP cc_start: 0.8384 (t0) cc_final: 0.7993 (t0) REVERT: B 380 ASP cc_start: 0.8580 (t0) cc_final: 0.8347 (t0) REVERT: B 390 ASP cc_start: 0.7345 (p0) cc_final: 0.7080 (p0) REVERT: C 144 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8680 (tp) REVERT: C 181 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.6472 (p90) REVERT: C 232 MET cc_start: 0.7843 (tpt) cc_final: 0.7216 (tpp) REVERT: C 285 MET cc_start: 0.8276 (mmm) cc_final: 0.7909 (mmm) outliers start: 44 outliers final: 33 residues processed: 186 average time/residue: 0.0914 time to fit residues: 25.6806 Evaluate side-chains 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 496 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 142 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN C 120 HIS ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.153163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114885 restraints weight = 12638.413| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.56 r_work: 0.2922 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12009 Z= 0.186 Angle : 0.570 9.881 16383 Z= 0.299 Chirality : 0.042 0.138 1890 Planarity : 0.004 0.039 1974 Dihedral : 4.300 21.044 1550 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.15 % Allowed : 22.11 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1485 helix: 1.50 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -0.45 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 175 TYR 0.009 0.001 TYR B 322 PHE 0.022 0.002 PHE C 122 TRP 0.027 0.001 TRP B 329 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00450 (12009) covalent geometry : angle 0.57009 (16383) hydrogen bonds : bond 0.04481 ( 909) hydrogen bonds : angle 4.56604 ( 2670) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.426 Fit side-chains REVERT: A 22 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6909 (mt) REVERT: A 116 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: A 285 MET cc_start: 0.8050 (mmm) cc_final: 0.7678 (mmt) REVERT: A 339 ARG cc_start: 0.7545 (mpt-90) cc_final: 0.7150 (mmt90) REVERT: A 425 ASP cc_start: 0.8305 (t0) cc_final: 0.7973 (m-30) REVERT: A 496 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7448 (mp) REVERT: B 156 MET cc_start: 0.8625 (mmm) cc_final: 0.8388 (mmm) REVERT: B 273 LEU cc_start: 0.7796 (tp) cc_final: 0.7194 (mt) REVERT: B 301 ASP cc_start: 0.8294 (t0) cc_final: 0.7841 (t0) REVERT: B 380 ASP cc_start: 0.8510 (t0) cc_final: 0.8242 (t0) REVERT: B 383 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8026 (mtm) REVERT: B 390 ASP cc_start: 0.7267 (p0) cc_final: 0.6982 (p0) REVERT: C 144 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8505 (tp) REVERT: C 181 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6370 (p90) REVERT: C 232 MET cc_start: 0.7724 (tpt) cc_final: 0.7086 (tpp) REVERT: C 233 MET cc_start: 0.7160 (mpp) cc_final: 0.6912 (mtm) REVERT: C 285 MET cc_start: 0.8029 (mmm) cc_final: 0.7621 (mmm) outliers start: 51 outliers final: 39 residues processed: 183 average time/residue: 0.0948 time to fit residues: 26.0021 Evaluate side-chains 186 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 496 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.109550 restraints weight = 12766.576| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.73 r_work: 0.3040 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12009 Z= 0.153 Angle : 0.553 9.500 16383 Z= 0.289 Chirality : 0.041 0.136 1890 Planarity : 0.004 0.039 1974 Dihedral : 4.262 22.286 1550 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.82 % Allowed : 22.11 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.21), residues: 1485 helix: 1.56 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.52 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 175 TYR 0.006 0.001 TYR B 322 PHE 0.041 0.002 PHE A 417 TRP 0.022 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00363 (12009) covalent geometry : angle 0.55318 (16383) hydrogen bonds : bond 0.04300 ( 909) hydrogen bonds : angle 4.51399 ( 2670) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.364 Fit side-chains REVERT: A 22 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7464 (mt) REVERT: A 116 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8718 (tt0) REVERT: A 181 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6391 (p90) REVERT: A 285 MET cc_start: 0.8457 (mmm) cc_final: 0.8102 (mmt) REVERT: A 425 ASP cc_start: 0.8560 (t0) cc_final: 0.8285 (m-30) REVERT: A 496 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8072 (mp) REVERT: B 273 LEU cc_start: 0.8236 (tp) cc_final: 0.7653 (mt) REVERT: B 301 ASP cc_start: 0.8514 (t0) cc_final: 0.8181 (t0) REVERT: B 339 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7580 (mtm-85) REVERT: B 383 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8284 (mtm) REVERT: B 390 ASP cc_start: 0.7420 (p0) cc_final: 0.7151 (p0) REVERT: C 144 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8756 (tp) REVERT: C 181 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6580 (p90) REVERT: C 232 MET cc_start: 0.7897 (tpt) cc_final: 0.7256 (tpp) REVERT: C 233 MET cc_start: 0.7497 (mpp) cc_final: 0.7256 (mtm) REVERT: C 285 MET cc_start: 0.8394 (mmm) cc_final: 0.8052 (mmm) outliers start: 47 outliers final: 37 residues processed: 181 average time/residue: 0.0902 time to fit residues: 24.6316 Evaluate side-chains 189 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 496 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.152145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.109807 restraints weight = 12628.534| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.73 r_work: 0.3045 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12009 Z= 0.140 Angle : 0.543 8.568 16383 Z= 0.284 Chirality : 0.041 0.140 1890 Planarity : 0.004 0.040 1974 Dihedral : 4.210 19.131 1550 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.66 % Allowed : 22.68 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.22), residues: 1485 helix: 1.60 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.49 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 175 TYR 0.005 0.001 TYR B 295 PHE 0.022 0.001 PHE A 420 TRP 0.020 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00324 (12009) covalent geometry : angle 0.54253 (16383) hydrogen bonds : bond 0.04182 ( 909) hydrogen bonds : angle 4.47367 ( 2670) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.331 Fit side-chains REVERT: A 22 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7382 (mt) REVERT: A 116 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: A 181 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6209 (p90) REVERT: A 285 MET cc_start: 0.8182 (mmm) cc_final: 0.7833 (mmt) REVERT: A 425 ASP cc_start: 0.8463 (t0) cc_final: 0.8183 (m-30) REVERT: A 496 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7972 (mp) REVERT: B 273 LEU cc_start: 0.8159 (tp) cc_final: 0.7603 (mt) REVERT: B 339 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7515 (mtm-85) REVERT: B 383 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8118 (mtm) REVERT: C 144 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8691 (tp) REVERT: C 181 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6428 (p90) REVERT: C 232 MET cc_start: 0.7791 (tpt) cc_final: 0.7174 (tpp) REVERT: C 233 MET cc_start: 0.7458 (mpp) cc_final: 0.7212 (mtm) REVERT: C 285 MET cc_start: 0.8118 (mmm) cc_final: 0.7774 (mmm) outliers start: 45 outliers final: 36 residues processed: 172 average time/residue: 0.0916 time to fit residues: 23.7952 Evaluate side-chains 183 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 496 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.151745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109578 restraints weight = 12738.311| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.72 r_work: 0.3041 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12009 Z= 0.149 Angle : 0.551 9.310 16383 Z= 0.288 Chirality : 0.041 0.143 1890 Planarity : 0.004 0.039 1974 Dihedral : 4.219 20.068 1550 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.74 % Allowed : 22.52 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.22), residues: 1485 helix: 1.59 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.49 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 175 TYR 0.006 0.001 TYR B 322 PHE 0.040 0.002 PHE A 417 TRP 0.022 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00350 (12009) covalent geometry : angle 0.55128 (16383) hydrogen bonds : bond 0.04235 ( 909) hydrogen bonds : angle 4.47687 ( 2670) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2970 Ramachandran restraints generated. 1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.444 Fit side-chains REVERT: A 22 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7402 (mt) REVERT: A 116 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8632 (tt0) REVERT: A 181 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6311 (p90) REVERT: A 285 MET cc_start: 0.8134 (mmm) cc_final: 0.7789 (mmt) REVERT: A 425 ASP cc_start: 0.8447 (t0) cc_final: 0.8176 (m-30) REVERT: A 496 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 273 LEU cc_start: 0.8166 (tp) cc_final: 0.7608 (mt) REVERT: B 383 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8122 (mtm) REVERT: C 144 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8661 (tp) REVERT: C 174 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: C 181 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6489 (p90) REVERT: C 232 MET cc_start: 0.7781 (tpt) cc_final: 0.7148 (tpp) REVERT: C 233 MET cc_start: 0.7456 (mpp) cc_final: 0.7202 (mtm) REVERT: C 285 MET cc_start: 0.8093 (mmm) cc_final: 0.7755 (mmm) outliers start: 46 outliers final: 37 residues processed: 174 average time/residue: 0.0869 time to fit residues: 22.8886 Evaluate side-chains 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 329 TRP Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 181 PHE Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 496 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 117 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116469 restraints weight = 12719.130| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.50 r_work: 0.2872 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12009 Z= 0.161 Angle : 0.563 9.289 16383 Z= 0.294 Chirality : 0.042 0.140 1890 Planarity : 0.004 0.039 1974 Dihedral : 4.246 19.738 1550 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.74 % Allowed : 22.68 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.21), residues: 1485 helix: 1.56 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.50 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 175 TYR 0.007 0.001 TYR B 322 PHE 0.022 0.002 PHE A 420 TRP 0.024 0.001 TRP B 329 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00384 (12009) covalent geometry : angle 0.56326 (16383) hydrogen bonds : bond 0.04314 ( 909) hydrogen bonds : angle 4.50682 ( 2670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.56 seconds wall clock time: 45 minutes 34.19 seconds (2734.19 seconds total)