Starting phenix.real_space_refine on Sat Nov 16 17:05:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zw8_60519/11_2024/8zw8_60519.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zw8_60519/11_2024/8zw8_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zw8_60519/11_2024/8zw8_60519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zw8_60519/11_2024/8zw8_60519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zw8_60519/11_2024/8zw8_60519.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zw8_60519/11_2024/8zw8_60519.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 7.15, per 1000 atoms: 0.61 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: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.09 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: 3.55 Time building geometry restraints manager: 3.59 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: 0.00 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: 0.750 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.330 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.040 ------------------------------------------------------------------------------- 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= 0.199 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 : 9.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (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 TRP 0.041 0.001 TRP B 329 HIS 0.002 0.001 HIS B 120 PHE 0.028 0.001 PHE C 417 TYR 0.005 0.001 TYR C 295 ARG 0.008 0.001 ARG A 175 *********************** 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 : 1.328 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: 0.2326 time to fit residues: 54.4536 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 : 1.352 ------------------------------------------------------------------------------- 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 124 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0671 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= 0.232 Angle : 0.559 8.750 16383 Z= 0.296 Chirality : 0.041 0.138 1890 Planarity : 0.004 0.041 1974 Dihedral : 4.680 41.742 1559 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.11 % Allowed : 24.55 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1485 helix: 1.54 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.36 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 329 HIS 0.003 0.001 HIS A 187 PHE 0.026 0.002 PHE A 417 TYR 0.009 0.001 TYR B 322 ARG 0.006 0.000 ARG B 175 *********************** 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 188 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.023 Fit side-chains REVERT: A 175 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.6593 (ttm-80) REVERT: A 232 MET cc_start: 0.7254 (tpp) cc_final: 0.6333 (ttm) REVERT: A 380 ASP cc_start: 0.8861 (t0) cc_final: 0.8607 (t0) REVERT: A 425 ASP cc_start: 0.8201 (t0) cc_final: 0.7898 (m-30) REVERT: B 273 LEU cc_start: 0.8023 (tp) cc_final: 0.7450 (mt) REVERT: B 301 ASP cc_start: 0.8347 (t0) cc_final: 0.7904 (t0) REVERT: B 380 ASP cc_start: 0.8689 (t0) cc_final: 0.8448 (t0) REVERT: B 390 ASP cc_start: 0.7294 (p0) cc_final: 0.6949 (p0) REVERT: C 22 ILE cc_start: 0.7321 (mm) cc_final: 0.7089 (mt) REVERT: C 232 MET cc_start: 0.7750 (tpt) cc_final: 0.7101 (tpp) outliers start: 26 outliers final: 17 residues processed: 186 average time/residue: 0.2055 time to fit residues: 57.4790 Evaluate side-chains 170 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL 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 422 THR 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 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0900 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= 0.226 Angle : 0.544 8.908 16383 Z= 0.287 Chirality : 0.041 0.136 1890 Planarity : 0.004 0.041 1974 Dihedral : 4.227 18.674 1550 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.93 % Allowed : 23.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1485 helix: 1.61 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.45 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 329 HIS 0.003 0.001 HIS A 187 PHE 0.024 0.002 PHE C 122 TYR 0.008 0.001 TYR B 322 ARG 0.005 0.000 ARG B 175 *********************** 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 195 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.165 Fit side-chains REVERT: A 22 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6988 (mt) REVERT: A 175 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.6708 (ttm-80) REVERT: A 425 ASP cc_start: 0.8202 (t0) cc_final: 0.7904 (m-30) REVERT: B 273 LEU cc_start: 0.8030 (tp) cc_final: 0.7437 (mt) REVERT: B 301 ASP cc_start: 0.8330 (t0) cc_final: 0.7907 (t0) REVERT: B 380 ASP cc_start: 0.8649 (t0) cc_final: 0.8391 (t0) REVERT: C 22 ILE cc_start: 0.7389 (mm) cc_final: 0.7171 (mt) REVERT: C 232 MET cc_start: 0.7724 (tpt) cc_final: 0.7118 (tpp) outliers start: 36 outliers final: 30 residues processed: 187 average time/residue: 0.2168 time to fit residues: 60.8351 Evaluate side-chains 182 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 265 MET 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 496 LEU 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 132 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 127 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12009 Z= 0.215 Angle : 0.532 8.665 16383 Z= 0.281 Chirality : 0.040 0.134 1890 Planarity : 0.004 0.041 1974 Dihedral : 4.198 18.717 1550 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.01 % Allowed : 23.74 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1485 helix: 1.65 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.50 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 PHE 0.030 0.001 PHE A 417 TYR 0.007 0.001 TYR B 322 ARG 0.003 0.000 ARG B 175 *********************** 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 188 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 1.301 Fit side-chains REVERT: A 22 ILE cc_start: 0.7265 (mm) cc_final: 0.6994 (mt) REVERT: A 116 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8872 (tt0) REVERT: A 232 MET cc_start: 0.7226 (tpp) cc_final: 0.6192 (ttm) REVERT: A 425 ASP cc_start: 0.8206 (t0) cc_final: 0.7901 (m-30) REVERT: A 496 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7677 (mp) REVERT: B 156 MET cc_start: 0.8789 (mmm) cc_final: 0.8512 (mmp) REVERT: B 273 LEU cc_start: 0.8018 (tp) cc_final: 0.7409 (mt) REVERT: B 301 ASP cc_start: 0.8365 (t0) cc_final: 0.7947 (t0) REVERT: B 380 ASP cc_start: 0.8590 (t0) cc_final: 0.8345 (t0) REVERT: B 383 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: B 390 ASP cc_start: 0.7378 (p0) cc_final: 0.6943 (p0) REVERT: C 144 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8697 (tp) REVERT: C 232 MET cc_start: 0.7705 (tpt) cc_final: 0.7089 (tpp) REVERT: C 285 MET cc_start: 0.8307 (mmm) cc_final: 0.7972 (mmm) outliers start: 37 outliers final: 32 residues processed: 180 average time/residue: 0.2043 time to fit residues: 55.8465 Evaluate side-chains 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 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 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 265 MET Chi-restraints excluded: chain B residue 281 THR 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 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 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 118 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12009 Z= 0.355 Angle : 0.604 11.152 16383 Z= 0.317 Chirality : 0.044 0.145 1890 Planarity : 0.004 0.040 1974 Dihedral : 4.416 23.774 1550 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.90 % Allowed : 22.93 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.21), residues: 1485 helix: 1.38 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -0.46 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 329 HIS 0.004 0.001 HIS A 145 PHE 0.022 0.002 PHE C 122 TYR 0.013 0.001 TYR B 322 ARG 0.005 0.001 ARG A 175 *********************** 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 204 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 1.257 Fit side-chains REVERT: A 22 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7403 (mt) REVERT: A 285 MET cc_start: 0.8427 (mmm) cc_final: 0.8047 (mmt) REVERT: A 380 ASP cc_start: 0.8912 (t0) cc_final: 0.8604 (t0) REVERT: A 381 VAL cc_start: 0.8631 (t) cc_final: 0.8377 (m) REVERT: A 425 ASP cc_start: 0.8228 (t0) cc_final: 0.7923 (m-30) REVERT: A 496 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7678 (mp) REVERT: B 273 LEU cc_start: 0.8118 (tp) cc_final: 0.7481 (mt) REVERT: B 301 ASP cc_start: 0.8390 (t0) cc_final: 0.8024 (t0) REVERT: B 380 ASP cc_start: 0.8700 (t0) cc_final: 0.8473 (t0) REVERT: B 383 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8209 (mtm) REVERT: C 181 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6438 (p90) REVERT: C 232 MET cc_start: 0.7724 (tpt) cc_final: 0.7124 (tpp) REVERT: C 285 MET cc_start: 0.8419 (mmm) cc_final: 0.7996 (mmm) outliers start: 48 outliers final: 38 residues processed: 194 average time/residue: 0.2229 time to fit residues: 63.8254 Evaluate side-chains 199 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 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 124 THR 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 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 47 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12009 Z= 0.215 Angle : 0.537 8.727 16383 Z= 0.284 Chirality : 0.041 0.141 1890 Planarity : 0.004 0.039 1974 Dihedral : 4.255 19.113 1550 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.85 % Allowed : 23.33 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1485 helix: 1.56 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.51 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 329 HIS 0.004 0.001 HIS C 192 PHE 0.028 0.001 PHE A 417 TYR 0.006 0.001 TYR B 322 ARG 0.007 0.000 ARG A 175 *********************** 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 196 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.281 Fit side-chains REVERT: A 22 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7211 (mt) REVERT: A 285 MET cc_start: 0.8375 (mmm) cc_final: 0.8022 (mmt) REVERT: A 381 VAL cc_start: 0.8627 (t) cc_final: 0.8370 (m) REVERT: A 425 ASP cc_start: 0.8232 (t0) cc_final: 0.7925 (m-30) REVERT: A 496 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7701 (mp) REVERT: B 273 LEU cc_start: 0.8071 (tp) cc_final: 0.7448 (mt) REVERT: B 301 ASP cc_start: 0.8365 (t0) cc_final: 0.7994 (t0) REVERT: B 380 ASP cc_start: 0.8598 (t0) cc_final: 0.8384 (t0) REVERT: B 390 ASP cc_start: 0.7464 (p0) cc_final: 0.7199 (p0) REVERT: C 144 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8681 (tp) REVERT: C 232 MET cc_start: 0.7706 (tpt) cc_final: 0.7127 (tpp) outliers start: 35 outliers final: 29 residues processed: 188 average time/residue: 0.2402 time to fit residues: 66.6974 Evaluate side-chains 188 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 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 42 TRP Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 144 LEU 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 16 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12009 Z= 0.203 Angle : 0.532 8.557 16383 Z= 0.281 Chirality : 0.040 0.156 1890 Planarity : 0.004 0.040 1974 Dihedral : 4.188 18.689 1550 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.17 % Allowed : 23.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1485 helix: 1.62 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.49 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 PHE 0.021 0.001 PHE C 122 TYR 0.005 0.001 TYR B 295 ARG 0.007 0.000 ARG A 175 *********************** 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 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.352 Fit side-chains REVERT: A 22 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7183 (mt) REVERT: A 116 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8840 (tt0) REVERT: A 285 MET cc_start: 0.8461 (mmm) cc_final: 0.8071 (mmt) REVERT: A 425 ASP cc_start: 0.8223 (t0) cc_final: 0.7928 (m-30) REVERT: A 496 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7709 (mp) REVERT: B 156 MET cc_start: 0.8786 (mmm) cc_final: 0.8403 (mmp) REVERT: B 273 LEU cc_start: 0.8016 (tp) cc_final: 0.7399 (mt) REVERT: C 232 MET cc_start: 0.7705 (tpt) cc_final: 0.7104 (tpp) REVERT: C 233 MET cc_start: 0.7132 (mpp) cc_final: 0.6864 (mtm) REVERT: C 285 MET cc_start: 0.8262 (mmm) cc_final: 0.7934 (mmm) outliers start: 39 outliers final: 32 residues processed: 180 average time/residue: 0.2213 time to fit residues: 58.6740 Evaluate side-chains 178 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 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 210 LEU 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 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 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 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 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1427 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= 0.264 Angle : 0.563 9.501 16383 Z= 0.295 Chirality : 0.042 0.146 1890 Planarity : 0.004 0.039 1974 Dihedral : 4.251 20.444 1550 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.58 % Allowed : 22.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1485 helix: 1.54 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.51 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 329 HIS 0.003 0.001 HIS A 149 PHE 0.032 0.002 PHE A 417 TYR 0.008 0.001 TYR B 322 ARG 0.008 0.001 ARG A 175 *********************** 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 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 1.226 Fit side-chains REVERT: A 22 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7227 (mt) REVERT: A 181 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6254 (p90) REVERT: A 285 MET cc_start: 0.8448 (mmm) cc_final: 0.8097 (mmt) REVERT: A 339 ARG cc_start: 0.7754 (mpt-90) cc_final: 0.7336 (mmt90) REVERT: A 425 ASP cc_start: 0.8238 (t0) cc_final: 0.7940 (m-30) REVERT: A 496 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7712 (mp) REVERT: B 273 LEU cc_start: 0.8077 (tp) cc_final: 0.7462 (mt) REVERT: B 301 ASP cc_start: 0.8400 (t0) cc_final: 0.8028 (t0) REVERT: B 383 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8186 (mtm) REVERT: B 390 ASP cc_start: 0.7482 (p0) cc_final: 0.7191 (p0) REVERT: C 22 ILE cc_start: 0.7427 (mm) cc_final: 0.7172 (mt) REVERT: C 144 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8674 (tp) REVERT: C 181 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6422 (p90) REVERT: C 232 MET cc_start: 0.7715 (tpt) cc_final: 0.7106 (tpp) REVERT: C 233 MET cc_start: 0.7256 (mpp) cc_final: 0.7000 (mtm) REVERT: C 285 MET cc_start: 0.8317 (mmm) cc_final: 0.7988 (mmm) outliers start: 44 outliers final: 34 residues processed: 186 average time/residue: 0.2310 time to fit residues: 64.1113 Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 140 GLN 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 281 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 0.0050 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12009 Z= 0.216 Angle : 0.541 8.605 16383 Z= 0.285 Chirality : 0.041 0.138 1890 Planarity : 0.004 0.039 1974 Dihedral : 4.190 18.661 1550 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.58 % Allowed : 22.52 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.22), residues: 1485 helix: 1.61 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.49 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 PHE 0.022 0.001 PHE A 420 TYR 0.005 0.001 TYR B 295 ARG 0.008 0.001 ARG A 175 *********************** 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 186 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 1.223 Fit side-chains REVERT: A 22 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7201 (mt) REVERT: A 181 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6167 (p90) REVERT: A 285 MET cc_start: 0.8459 (mmm) cc_final: 0.8082 (mmt) REVERT: A 425 ASP cc_start: 0.8228 (t0) cc_final: 0.7920 (m-30) REVERT: A 496 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7711 (mp) REVERT: B 273 LEU cc_start: 0.8050 (tp) cc_final: 0.7444 (mt) REVERT: B 383 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8102 (mtm) REVERT: C 22 ILE cc_start: 0.7433 (mm) cc_final: 0.7215 (mt) REVERT: C 144 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8666 (tp) REVERT: C 181 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6385 (p90) REVERT: C 232 MET cc_start: 0.7710 (tpt) cc_final: 0.7101 (tpp) REVERT: C 233 MET cc_start: 0.7264 (mpp) cc_final: 0.6984 (mtm) REVERT: C 285 MET cc_start: 0.8303 (mmm) cc_final: 0.7969 (mmm) outliers start: 44 outliers final: 36 residues processed: 175 average time/residue: 0.2237 time to fit residues: 59.1070 Evaluate side-chains 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 140 GLN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 210 LEU 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 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 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: 0.7980 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1449 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= 0.220 Angle : 0.547 9.294 16383 Z= 0.287 Chirality : 0.041 0.140 1890 Planarity : 0.004 0.039 1974 Dihedral : 4.185 19.046 1550 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.58 % Allowed : 22.52 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1485 helix: 1.61 (0.15), residues: 1179 sheet: None (None), residues: 0 loop : -0.46 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 PHE 0.038 0.001 PHE A 417 TYR 0.006 0.001 TYR B 322 ARG 0.009 0.001 ARG A 175 ********************** 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: 44 poor density : 143 time to evaluate : 1.480 Fit side-chains REVERT: A 22 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7207 (mt) REVERT: A 181 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6201 (p90) REVERT: A 285 MET cc_start: 0.8432 (mmm) cc_final: 0.8085 (mmt) REVERT: A 425 ASP cc_start: 0.8229 (t0) cc_final: 0.7929 (m-30) REVERT: A 496 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7711 (mp) REVERT: B 273 LEU cc_start: 0.8018 (tp) cc_final: 0.7412 (mt) REVERT: B 383 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8159 (mtm) REVERT: C 22 ILE cc_start: 0.7435 (mm) cc_final: 0.7226 (mt) REVERT: C 144 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8635 (tp) REVERT: C 181 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6407 (p90) REVERT: C 232 MET cc_start: 0.7699 (tpt) cc_final: 0.7066 (tpp) REVERT: C 233 MET cc_start: 0.7259 (mpp) cc_final: 0.6982 (mtm) REVERT: C 285 MET cc_start: 0.8296 (mmm) cc_final: 0.7961 (mmm) outliers start: 44 outliers final: 36 residues processed: 176 average time/residue: 0.2231 time to fit residues: 58.3412 Evaluate side-chains 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 109 ILE 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 281 THR 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 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 124 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 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 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.155819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117267 restraints weight = 12565.806| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.55 r_work: 0.2943 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12009 Z= 0.209 Angle : 0.541 9.126 16383 Z= 0.284 Chirality : 0.041 0.139 1890 Planarity : 0.004 0.039 1974 Dihedral : 4.158 18.376 1550 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.66 % Allowed : 22.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1485 helix: 1.66 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -0.49 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 329 HIS 0.002 0.001 HIS A 149 PHE 0.021 0.001 PHE A 420 TYR 0.006 0.001 TYR B 295 ARG 0.009 0.001 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.31 seconds wall clock time: 47 minutes 0.33 seconds (2820.33 seconds total)