Starting phenix.real_space_refine
on Wed Feb  4 05:48:02 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9nhe_49410/02_2026/9nhe_49410.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nhe_49410/02_2026/9nhe_49410.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nhe_49410/02_2026/9nhe_49410.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nhe_49410/02_2026/9nhe_49410.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nhe_49410/02_2026/9nhe_49410.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nhe_49410/02_2026/9nhe_49410.cif"
  }
  resolution = 4.2
  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=   0.001 sd=   0.043
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: 6
    Type Number    sf(0)   Gaussians
     P      44      5.49       5
     Mg      1      5.21       5
     S      39      5.16       5
     C    5443      2.51       5
     N    1501      2.21       5
     O    1750      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8778
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 736, 5941
          Classifications: {'peptide': 736}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 35, 'TRANS': 700}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 476
          Classifications: {'RNA': 22}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 2, 'rna3p': 19}
    Chain: "C"
      Number of atoms: 459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 459
          Classifications: {'RNA': 22}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 2, 'rna3p': 19}
    Chain: "F"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1901
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 13, 'TRANS': 222}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.19, per 1000 atoms: 0.25
  Number of scatterers: 8778
  At special positions: 0
  Unit cell: (106.47, 89.18, 108.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      44     15.00
     Mg      1     11.99
     O    1750      8.00
     N    1501      7.00
     C    5443      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: 0.90
  Conformation dependent library (CDL) restraints added in 335.2 milliseconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1842

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 11 sheets defined
      40.4% alpha, 17.5% beta
      14 base pairs and 26 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 181 through 190
      removed outlier: 3.564A  pdb=" N   ARG A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 197
      removed outlier: 3.625A  pdb=" N   LEU A 196 " --> pdb=" O   HIS A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 262
    Processing helix  chain 'A' and resid 281 through 283
      No H-bonds generated for 'chain 'A' and resid 281 through 283'
    Processing helix  chain 'A' and resid 317 through 329
    Processing helix  chain 'A' and resid 333 through 342
    Processing helix  chain 'A' and resid 379 through 388
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.966A  pdb=" N   ARG A 409 " --> pdb=" O   PRO A 405 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ALA A 410 " --> pdb=" O   ARG A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 421
      No H-bonds generated for 'chain 'A' and resid 419 through 421'
    Processing helix  chain 'A' and resid 431 through 434
      removed outlier: 4.052A  pdb=" N   ALA A 434 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 431 through 434'
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.632A  pdb=" N   MET A 439 " --> pdb=" O   ASN A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 467
    Processing helix  chain 'A' and resid 467 through 477
      removed outlier: 3.502A  pdb=" N   VAL A 471 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 522
      removed outlier: 3.568A  pdb=" N   THR A 516 " --> pdb=" O   GLU A 513 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ARG A 517 " --> pdb=" O   GLY A 514 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   ASP A 518 " --> pdb=" O   TRP A 515 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   MET A 519 " --> pdb=" O   THR A 516 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ARG A 520 " --> pdb=" O   ARG A 517 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER A 521 " --> pdb=" O   ASP A 518 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LYS A 522 " --> pdb=" O   MET A 519 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 513 through 522'
    Processing helix  chain 'A' and resid 541 through 560
    Processing helix  chain 'A' and resid 575 through 590
    Processing helix  chain 'A' and resid 604 through 616
      removed outlier: 3.606A  pdb=" N   CYS A 614 " --> pdb=" O   ILE A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 650
      removed outlier: 3.505A  pdb=" N   LEU A 650 " --> pdb=" O   ILE A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 729
    Processing helix  chain 'A' and resid 743 through 745
      No H-bonds generated for 'chain 'A' and resid 743 through 745'
    Processing helix  chain 'A' and resid 746 through 752
    Processing helix  chain 'A' and resid 754 through 767
    Processing helix  chain 'A' and resid 842 through 853
    Processing helix  chain 'A' and resid 867 through 880
      removed outlier: 3.809A  pdb=" N   GLN A 871 " --> pdb=" O   PRO A 867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 893
      removed outlier: 3.708A  pdb=" N   ASN A 893 " --> pdb=" O   TYR A 890 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 110
      removed outlier: 3.766A  pdb=" N   GLU F  93 " --> pdb=" O   MET F  89 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ASP F  94 " --> pdb=" O   LYS F  90 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP F  99 " --> pdb=" O   ASN F  95 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN F 101 " --> pdb=" O   LYS F  97 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 112 through 115
    Processing helix  chain 'F' and resid 166 through 178
    Processing helix  chain 'F' and resid 190 through 199
    Processing helix  chain 'F' and resid 218 through 233
      removed outlier: 3.740A  pdb=" N   ASP F 223 " --> pdb=" O   PRO F 219 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   ALA F 224 " --> pdb=" O   GLU F 220 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 248 through 260
    Processing helix  chain 'F' and resid 271 through 279
      removed outlier: 4.064A  pdb=" N   THR F 275 " --> pdb=" O   SER F 271 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 290 through 296
      removed outlier: 3.652A  pdb=" N   GLU F 294 " --> pdb=" O   CYS F 290 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   SER F 295 " --> pdb=" O   GLU F 291 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 302 through 323
      removed outlier: 4.019A  pdb=" N   ARG F 317 " --> pdb=" O   THR F 313 " (cutoff:3.500A)
      Proline residue:  F 320  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 488
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267
    Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 267
      removed outlier: 3.575A  pdb=" N   THR A 294 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASN A 296 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 303 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   LEU A 302 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU A 161 " --> pdb=" O   LYS A 480 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   LYS A 480 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 208
      removed outlier: 3.663A  pdb=" N   ASP A 174 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   LEU A 233 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 356
    Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 372
      removed outlier: 3.551A  pdb=" N   GLU A 375 " --> pdb=" O   MET A 372 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 402
    Processing sheet with id=AA8, first strand: chain 'A' and resid 491 through 492
      removed outlier: 3.570A  pdb=" N   ARG A 491 " --> pdb=" O   VAL A 802 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 801 " --> pdb=" O   VAL A 818 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER A 831 " --> pdb=" O   SER A 779 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ILE A 735 " --> pdb=" O   ALA A 774 " (cutoff:3.500A)
      removed outlier: 7.791A  pdb=" N   ILE A 776 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   ILE A 737 " --> pdb=" O   ILE A 776 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   VAL A 778 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ARG A 739 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 500
      removed outlier: 3.553A  pdb=" N   GLN A 500 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 504 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 569 through 571
      removed outlier: 7.903A  pdb=" N   VAL A 569 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 535 " --> pdb=" O   VAL A 569 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   ILE A 571 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   THR A 537 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE A 595 " --> pdb=" O   GLN A 623 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   VAL A 625 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   CYS A 597 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 148 through 156
      removed outlier: 6.903A  pdb=" N   GLN F 142 " --> pdb=" O   LYS F 150 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 140 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   VAL F 140 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   HIS F 154 " --> pdb=" O   PHE F 138 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   PHE F 138 " --> pdb=" O   HIS F 154 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   THR F 156 " --> pdb=" O   GLY F 136 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   GLY F 136 " --> pdb=" O   THR F 156 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL F 120 " --> pdb=" O   THR F 141 " (cutoff:3.500A)
      removed outlier: 10.069A  pdb=" N   PHE F 216 " --> pdb=" O   ASP F 117 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   TYR F 119 " --> pdb=" O   PHE F 216 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   MET F 215 " --> pdb=" O   TYR F 246 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    906 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      37 hydrogen bonds
      74 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      26 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.32: 1542
        1.32 -     1.45: 2477
        1.45 -     1.57: 4882
        1.57 -     1.70: 86
        1.70 -     1.82: 61
  Bond restraints: 9048
  Sorted by residual:
  bond pdb=" CZ  ARG A 812 "
       pdb=" NH2 ARG A 812 "
    ideal  model  delta    sigma   weight residual
    1.330  1.282  0.048 1.30e-02 5.92e+03 1.35e+01
  bond pdb=" CA  PRO F 213 "
       pdb=" C   PRO F 213 "
    ideal  model  delta    sigma   weight residual
    1.514  1.534 -0.019 5.50e-03 3.31e+04 1.25e+01
  bond pdb=" N   VAL A 620 "
       pdb=" CA  VAL A 620 "
    ideal  model  delta    sigma   weight residual
    1.456  1.482 -0.026 8.70e-03 1.32e+04 8.85e+00
  bond pdb=" CZ  ARG A 256 "
       pdb=" NH2 ARG A 256 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.13e+00
  bond pdb=" CZ  ARG A 491 "
       pdb=" NH2 ARG A 491 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 7.90e+00
  ... (remaining 9043 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 10991
        2.33 -     4.67: 1286
        4.67 -     7.00: 155
        7.00 -     9.33: 16
        9.33 -    11.66: 4
  Bond angle restraints: 12452
  Sorted by residual:
  angle pdb=" C3'   C C  10 "
        pdb=" O3'   C C  10 "
        pdb=" P     C C  11 "
      ideal   model   delta    sigma   weight residual
     120.20  108.54   11.66 1.50e+00 4.44e-01 6.05e+01
  angle pdb=" C3'   C C   8 "
        pdb=" O3'   C C   8 "
        pdb=" P     A C   9 "
      ideal   model   delta    sigma   weight residual
     120.20  109.07   11.13 1.50e+00 4.44e-01 5.50e+01
  angle pdb=" C3'   A C   6 "
        pdb=" O3'   A C   6 "
        pdb=" P     A C   7 "
      ideal   model   delta    sigma   weight residual
     120.20  109.13   11.07 1.50e+00 4.44e-01 5.45e+01
  angle pdb=" C3'   C C   4 "
        pdb=" O3'   C C   4 "
        pdb=" P     A C   5 "
      ideal   model   delta    sigma   weight residual
     120.20  109.49   10.71 1.50e+00 4.44e-01 5.10e+01
  angle pdb=" CA  ASP F 280 "
        pdb=" CB  ASP F 280 "
        pdb=" CG  ASP F 280 "
      ideal   model   delta    sigma   weight residual
     112.60  118.94   -6.34 1.00e+00 1.00e+00 4.02e+01
  ... (remaining 12447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.89: 5197
       27.89 -    55.77: 265
       55.77 -    83.66: 68
       83.66 -   111.54: 5
      111.54 -   139.43: 1
  Dihedral angle restraints: 5536
    sinusoidal: 2681
      harmonic: 2855
  Sorted by residual:
  dihedral pdb=" C5'   U B   1 "
           pdb=" C4'   U B   1 "
           pdb=" C3'   U B   1 "
           pdb=" O3'   U B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   95.09   51.91     1      8.00e+00 1.56e-02 5.75e+01
  dihedral pdb=" O4'   C C   8 "
           pdb=" C2'   C C   8 "
           pdb=" C1'   C C   8 "
           pdb=" C3'   C C   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -25.84   50.84     1      8.00e+00 1.56e-02 5.53e+01
  dihedral pdb=" O4'   U B   1 "
           pdb=" C4'   U B   1 "
           pdb=" C3'   U B   1 "
           pdb=" C2'   U B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -19.90   43.90     1      8.00e+00 1.56e-02 4.19e+01
  ... (remaining 5533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.121: 1276
       0.121 -    0.243: 139
       0.243 -    0.364: 15
       0.364 -    0.485: 7
       0.485 -    0.607: 2
  Chirality restraints: 1439
  Sorted by residual:
  chirality pdb=" P     A C  25 "
            pdb=" OP1   A C  25 "
            pdb=" OP2   A C  25 "
            pdb=" O5'   A C  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.02   -0.61 2.00e-01 2.50e+01 9.20e+00
  chirality pdb=" P     U B   1 "
            pdb=" OP1   U B   1 "
            pdb=" OP2   U B   1 "
            pdb=" O5'   U B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.93   -0.52 2.00e-01 2.50e+01 6.79e+00
  chirality pdb=" P     A C   5 "
            pdb=" OP1   A C   5 "
            pdb=" OP2   A C   5 "
            pdb=" O5'   A C   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.81   -0.40 2.00e-01 2.50e+01 4.06e+00
  ... (remaining 1436 not shown)

  Planarity restraints: 1422
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C  14 "   -0.198 2.00e-02 2.50e+03   9.51e-02 2.03e+02
        pdb=" N1    U C  14 "    0.067 2.00e-02 2.50e+03
        pdb=" C2    U C  14 "    0.087 2.00e-02 2.50e+03
        pdb=" O2    U C  14 "    0.021 2.00e-02 2.50e+03
        pdb=" N3    U C  14 "    0.033 2.00e-02 2.50e+03
        pdb=" C4    U C  14 "   -0.023 2.00e-02 2.50e+03
        pdb=" O4    U C  14 "   -0.129 2.00e-02 2.50e+03
        pdb=" C5    U C  14 "    0.048 2.00e-02 2.50e+03
        pdb=" C6    U C  14 "    0.095 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  13 "    0.184 2.00e-02 2.50e+03   8.40e-02 1.94e+02
        pdb=" N9    A B  13 "    0.010 2.00e-02 2.50e+03
        pdb=" C8    A B  13 "   -0.098 2.00e-02 2.50e+03
        pdb=" N7    A B  13 "   -0.072 2.00e-02 2.50e+03
        pdb=" C5    A B  13 "   -0.019 2.00e-02 2.50e+03
        pdb=" C6    A B  13 "    0.044 2.00e-02 2.50e+03
        pdb=" N6    A B  13 "    0.123 2.00e-02 2.50e+03
        pdb=" N1    A B  13 "    0.012 2.00e-02 2.50e+03
        pdb=" C2    A B  13 "   -0.058 2.00e-02 2.50e+03
        pdb=" N3    A B  13 "   -0.076 2.00e-02 2.50e+03
        pdb=" C4    A B  13 "   -0.049 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  12 "    0.203 2.00e-02 2.50e+03   8.19e-02 1.84e+02
        pdb=" N9    A C  12 "   -0.065 2.00e-02 2.50e+03
        pdb=" C8    A C  12 "   -0.086 2.00e-02 2.50e+03
        pdb=" N7    A C  12 "   -0.020 2.00e-02 2.50e+03
        pdb=" C5    A C  12 "   -0.011 2.00e-02 2.50e+03
        pdb=" C6    A C  12 "    0.038 2.00e-02 2.50e+03
        pdb=" N6    A C  12 "    0.085 2.00e-02 2.50e+03
        pdb=" N1    A C  12 "    0.032 2.00e-02 2.50e+03
        pdb=" C2    A C  12 "   -0.040 2.00e-02 2.50e+03
        pdb=" N3    A C  12 "   -0.075 2.00e-02 2.50e+03
        pdb=" C4    A C  12 "   -0.060 2.00e-02 2.50e+03
  ... (remaining 1419 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 26
        2.48 -     3.09: 6012
        3.09 -     3.69: 13819
        3.69 -     4.30: 18517
        4.30 -     4.90: 30441
  Nonbonded interactions: 68815
  Sorted by model distance:
  nonbonded pdb=" OP1   U C  16 "
            pdb="MG    MG C 101 "
     model   vdw
     1.880 2.170
  nonbonded pdb=" O3'   G C  15 "
            pdb="MG    MG C 101 "
     model   vdw
     2.034 2.170
  nonbonded pdb=" OD1 ASP A 451 "
            pdb=" OG  SER A 793 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" NE2 HIS A 192 "
            pdb=" O   TYR A 220 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" O   ASP A 393 "
            pdb=" NE2 GLN A 396 "
     model   vdw
     2.280 3.120
  ... (remaining 68810 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
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:             1.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.310
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
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      :  0.009   0.048   9048  Z= 0.556
  Angle     :  1.492  11.663  12452  Z= 0.967
  Chirality :  0.084   0.607   1439
  Planarity :  0.013   0.125   1422
  Dihedral  : 17.066 139.426   3694
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  4.01 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.26), residues: 954
  helix: -0.44 (0.27), residues: 326
  sheet: -0.94 (0.38), residues: 169
  loop : -1.10 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 301 
 TYR   0.112   0.015   TYR A 607 
 PHE   0.061   0.008   PHE A 272 
 TRP   0.098   0.020   TRP A 655 
 HIS   0.010   0.002   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00940 ( 9048)
  covalent geometry    : angle       1.49246 (12452)
  hydrogen bonds       : bond        0.20558 (  349)
  hydrogen bonds       : angle       7.54556 (  980)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 296
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 ASN cc_start: 0.7904 (t0) cc_final: 0.7640 (t0)
REVERT: A  300 ASP cc_start: 0.7867 (m-30) cc_final: 0.6632 (m-30)
REVERT: A  302 LEU cc_start: 0.8678 (tp) cc_final: 0.8465 (mt)
REVERT: A  303 LEU cc_start: 0.8192 (mp) cc_final: 0.7962 (mp)
REVERT: A  385 LYS cc_start: 0.8894 (tmtt) cc_final: 0.8448 (mmtp)
REVERT: A  389 LEU cc_start: 0.8601 (mt) cc_final: 0.8223 (mp)
REVERT: A  404 LYS cc_start: 0.7967 (mmpt) cc_final: 0.7709 (mttm)
REVERT: A  412 LEU cc_start: 0.8865 (mm) cc_final: 0.8547 (mt)
REVERT: A  425 GLN cc_start: 0.7848 (tt0) cc_final: 0.7619 (mp10)
REVERT: A  608 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7914 (tm-30)
REVERT: A  625 VAL cc_start: 0.8494 (t) cc_final: 0.8170 (m)
REVERT: A  665 MET cc_start: 0.7292 (ttm) cc_final: 0.6684 (mtp)
REVERT: A  712 HIS cc_start: 0.4843 (t-90) cc_final: 0.4319 (t-170)
REVERT: A  734 ARG cc_start: 0.7312 (ttm110) cc_final: 0.6859 (mtt-85)
REVERT: A  760 LYS cc_start: 0.8989 (tptp) cc_final: 0.8543 (mptt)
REVERT: A  842 ASN cc_start: 0.7229 (t0) cc_final: 0.6942 (t0)
REVERT: F   89 MET cc_start: 0.6891 (mmp) cc_final: 0.6499 (mmm)
REVERT: F  100 ILE cc_start: 0.8279 (mm) cc_final: 0.8016 (mm)
REVERT: F  105 LYS cc_start: 0.7697 (pptt) cc_final: 0.7461 (mttp)
REVERT: F  135 ILE cc_start: 0.7072 (pt) cc_final: 0.6565 (mm)
REVERT: F  177 PHE cc_start: 0.6792 (m-80) cc_final: 0.6090 (m-80)
REVERT: F  195 LEU cc_start: 0.8411 (mm) cc_final: 0.7938 (mt)
REVERT: F  201 TYR cc_start: 0.7345 (t80) cc_final: 0.6657 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 299
  average time/residue: 0.1357
  time to fit residues: 51.3603
Evaluate side-chains
  180 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 HIS
A 249 GLN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 746 GLN
F 197 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.163579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.141586 restraints weight = 16119.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.142505 restraints weight = 12565.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.145361 restraints weight = 9503.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.146071 restraints weight = 6093.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.146673 restraints weight = 5792.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9048  Z= 0.164
  Angle     :  0.708   6.878  12452  Z= 0.377
  Chirality :  0.048   0.225   1439
  Planarity :  0.005   0.067   1422
  Dihedral  : 15.648 141.926   1741
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  3.67 %
    Favored  : 95.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.27), residues: 954
  helix:  0.06 (0.28), residues: 341
  sheet: -0.99 (0.38), residues: 193
  loop : -0.93 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 785 
 TYR   0.025   0.002   TYR A 291 
 PHE   0.018   0.002   PHE A 561 
 TRP   0.013   0.002   TRP A 533 
 HIS   0.008   0.001   HIS A 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9048)
  covalent geometry    : angle       0.70795 (12452)
  hydrogen bonds       : bond        0.05126 (  349)
  hydrogen bonds       : angle       5.31344 (  980)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 219
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7464 (ttpt) cc_final: 0.7055 (ttmt)
REVERT: A  381 GLU cc_start: 0.8523 (tt0) cc_final: 0.8281 (tp30)
REVERT: A  385 LYS cc_start: 0.8844 (tmtt) cc_final: 0.8612 (mmtp)
REVERT: A  404 LYS cc_start: 0.8297 (mmmt) cc_final: 0.8047 (mttt)
REVERT: A  568 LEU cc_start: 0.7446 (pt) cc_final: 0.7083 (pt)
REVERT: A  578 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7069 (mp0)
REVERT: A  665 MET cc_start: 0.6956 (ttm) cc_final: 0.6753 (mtp)
REVERT: A  760 LYS cc_start: 0.8781 (tptp) cc_final: 0.8485 (mptt)
REVERT: F   89 MET cc_start: 0.7097 (mmp) cc_final: 0.6609 (mmm)
REVERT: F  105 LYS cc_start: 0.7676 (pptt) cc_final: 0.7452 (mmtp)
REVERT: F  135 ILE cc_start: 0.7219 (pt) cc_final: 0.6757 (mm)
REVERT: F  149 VAL cc_start: 0.9236 (p) cc_final: 0.9036 (m)
REVERT: F  176 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7134 (pp20)
REVERT: F  201 TYR cc_start: 0.7603 (t80) cc_final: 0.6831 (t80)
  outliers start: 5
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1131
  time to fit residues: 33.4102
Evaluate side-chains
  158 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 80 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 77 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
A 458 ASN
A 459 ASN
F 227 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.151671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.129116 restraints weight = 16097.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.130572 restraints weight = 11477.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.132260 restraints weight = 9270.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.132632 restraints weight = 6583.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.132824 restraints weight = 6207.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   9048  Z= 0.258
  Angle     :  0.777   7.257  12452  Z= 0.408
  Chirality :  0.049   0.259   1439
  Planarity :  0.006   0.056   1422
  Dihedral  : 15.498 142.352   1741
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  8.02 %
    Favored  : 91.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.27), residues: 954
  helix:  0.10 (0.27), residues: 345
  sheet: -1.32 (0.36), residues: 190
  loop : -1.09 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 792 
 TYR   0.039   0.003   TYR A 291 
 PHE   0.017   0.002   PHE F 267 
 TRP   0.027   0.003   TRP A 533 
 HIS   0.005   0.001   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 ( 9048)
  covalent geometry    : angle       0.77738 (12452)
  hydrogen bonds       : bond        0.05473 (  349)
  hydrogen bonds       : angle       5.22999 (  980)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 202
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7610 (ttpt) cc_final: 0.7101 (ttmt)
REVERT: A  297 GLN cc_start: 0.8059 (tp40) cc_final: 0.7708 (tt0)
REVERT: A  303 LEU cc_start: 0.8889 (mp) cc_final: 0.8667 (mp)
REVERT: A  381 GLU cc_start: 0.8378 (tt0) cc_final: 0.8171 (tp30)
REVERT: A  385 LYS cc_start: 0.8735 (tmtt) cc_final: 0.8110 (mttm)
REVERT: A  404 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8185 (mttt)
REVERT: A  625 VAL cc_start: 0.8541 (t) cc_final: 0.8328 (m)
REVERT: A  667 VAL cc_start: 0.8724 (t) cc_final: 0.8524 (t)
REVERT: A  760 LYS cc_start: 0.8799 (tptp) cc_final: 0.8511 (mptt)
REVERT: F   89 MET cc_start: 0.7276 (mmp) cc_final: 0.6725 (mmm)
REVERT: F  119 TYR cc_start: 0.6368 (m-80) cc_final: 0.6087 (m-10)
REVERT: F  147 ASP cc_start: 0.7969 (t70) cc_final: 0.7538 (t0)
REVERT: F  177 PHE cc_start: 0.7042 (m-80) cc_final: 0.6610 (m-80)
  outliers start: 5
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1031
  time to fit residues: 28.7618
Evaluate side-chains
  145 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    0.2980
   chunk 23 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.2980
   chunk 54 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
A 458 ASN
A 602 ASN
F 227 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.158093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.135812 restraints weight = 16065.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.137989 restraints weight = 11691.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.139943 restraints weight = 8710.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.140292 restraints weight = 5741.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.140573 restraints weight = 5449.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.4894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9048  Z= 0.143
  Angle     :  0.647  10.817  12452  Z= 0.338
  Chirality :  0.046   0.242   1439
  Planarity :  0.005   0.053   1422
  Dihedral  : 15.292 143.209   1741
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.32 %
    Favored  : 96.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.27), residues: 954
  helix:  0.13 (0.27), residues: 347
  sheet: -0.99 (0.38), residues: 186
  loop : -1.00 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 520 
 TYR   0.032   0.002   TYR A 291 
 PHE   0.037   0.002   PHE F 312 
 TRP   0.017   0.002   TRP A 533 
 HIS   0.004   0.001   HIS F 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9048)
  covalent geometry    : angle       0.64697 (12452)
  hydrogen bonds       : bond        0.04470 (  349)
  hydrogen bonds       : angle       4.93081 (  980)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 GLU cc_start: 0.7455 (pm20) cc_final: 0.6985 (mm-30)
REVERT: A  292 LYS cc_start: 0.7607 (ttpt) cc_final: 0.7140 (ttmt)
REVERT: A  303 LEU cc_start: 0.8869 (mp) cc_final: 0.8639 (mp)
REVERT: A  381 GLU cc_start: 0.8347 (tt0) cc_final: 0.7983 (mm-30)
REVERT: A  385 LYS cc_start: 0.8538 (tmtt) cc_final: 0.8093 (mmtp)
REVERT: A  404 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8155 (mttt)
REVERT: A  578 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7216 (mp0)
REVERT: A  760 LYS cc_start: 0.8795 (tptp) cc_final: 0.8484 (mptt)
REVERT: F   89 MET cc_start: 0.7266 (mmp) cc_final: 0.6734 (mmm)
REVERT: F  135 ILE cc_start: 0.7660 (mm) cc_final: 0.7457 (mm)
REVERT: F  147 ASP cc_start: 0.7675 (t70) cc_final: 0.7349 (t0)
REVERT: F  177 PHE cc_start: 0.6887 (m-80) cc_final: 0.6396 (m-80)
REVERT: F  195 LEU cc_start: 0.8154 (mm) cc_final: 0.7903 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 207
  average time/residue: 0.1005
  time to fit residues: 28.5937
Evaluate side-chains
  149 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 57 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0020
   chunk 47 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0170
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.8828

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
F 227 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.156947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.134650 restraints weight = 16158.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.135913 restraints weight = 11860.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.138054 restraints weight = 9391.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.138884 restraints weight = 6441.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.139502 restraints weight = 6129.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.5294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9048  Z= 0.138
  Angle     :  0.618   8.087  12452  Z= 0.322
  Chirality :  0.045   0.241   1439
  Planarity :  0.004   0.049   1422
  Dihedral  : 15.139 144.002   1741
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.41 %
    Favored  : 97.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.27), residues: 954
  helix:  0.30 (0.28), residues: 348
  sheet: -1.05 (0.36), residues: 198
  loop : -0.92 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 309 
 TYR   0.029   0.002   TYR A 291 
 PHE   0.028   0.002   PHE F 312 
 TRP   0.013   0.002   TRP F 310 
 HIS   0.003   0.001   HIS A 855 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9048)
  covalent geometry    : angle       0.61768 (12452)
  hydrogen bonds       : bond        0.04152 (  349)
  hydrogen bonds       : angle       4.75393 (  980)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 198
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ARG cc_start: 0.7443 (mtp-110) cc_final: 0.6328 (mtp-110)
REVERT: A  292 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7177 (ttmt)
REVERT: A  303 LEU cc_start: 0.8930 (mp) cc_final: 0.8695 (mp)
REVERT: A  381 GLU cc_start: 0.8352 (tt0) cc_final: 0.8006 (mm-30)
REVERT: A  385 LYS cc_start: 0.8562 (tmtt) cc_final: 0.8089 (mmtp)
REVERT: A  404 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8117 (mttt)
REVERT: A  578 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7104 (mp0)
REVERT: A  760 LYS cc_start: 0.8858 (tptp) cc_final: 0.8505 (mptt)
REVERT: F   89 MET cc_start: 0.7329 (mmp) cc_final: 0.6916 (mmt)
REVERT: F  177 PHE cc_start: 0.6827 (m-80) cc_final: 0.6451 (m-80)
REVERT: F  285 THR cc_start: 0.7900 (p) cc_final: 0.7675 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0944
  time to fit residues: 26.2654
Evaluate side-chains
  145 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 86 optimal weight:    9.9990
   chunk 16 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 227 ASN
F 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.155965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.133863 restraints weight = 16044.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.135349 restraints weight = 12231.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.137196 restraints weight = 9549.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.138362 restraints weight = 6322.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.138562 restraints weight = 5878.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.5551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9048  Z= 0.148
  Angle     :  0.635   8.199  12452  Z= 0.331
  Chirality :  0.045   0.241   1439
  Planarity :  0.005   0.046   1422
  Dihedral  : 15.044 145.181   1741
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.28), residues: 954
  helix:  0.35 (0.28), residues: 348
  sheet: -1.17 (0.36), residues: 195
  loop : -0.86 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 406 
 TYR   0.026   0.002   TYR A 291 
 PHE   0.014   0.001   PHE F 143 
 TRP   0.016   0.002   TRP F 310 
 HIS   0.006   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9048)
  covalent geometry    : angle       0.63523 (12452)
  hydrogen bonds       : bond        0.04200 (  349)
  hydrogen bonds       : angle       4.77585 (  980)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ARG cc_start: 0.7431 (mtp-110) cc_final: 0.6273 (mtp-110)
REVERT: A  292 LYS cc_start: 0.7568 (ttpt) cc_final: 0.7257 (ttpt)
REVERT: A  303 LEU cc_start: 0.8995 (mp) cc_final: 0.8748 (mp)
REVERT: A  324 GLU cc_start: 0.7865 (pp20) cc_final: 0.7532 (tm-30)
REVERT: A  381 GLU cc_start: 0.8316 (tt0) cc_final: 0.7951 (mm-30)
REVERT: A  385 LYS cc_start: 0.8576 (tmtt) cc_final: 0.8048 (mmtp)
REVERT: A  404 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8075 (mttt)
REVERT: A  515 TRP cc_start: 0.8394 (p90) cc_final: 0.7776 (p90)
REVERT: A  578 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7213 (mp0)
REVERT: A  760 LYS cc_start: 0.8813 (tptp) cc_final: 0.8485 (mptt)
REVERT: A  861 SER cc_start: 0.8896 (p) cc_final: 0.8539 (p)
REVERT: F  147 ASP cc_start: 0.7799 (t70) cc_final: 0.7469 (t0)
REVERT: F  177 PHE cc_start: 0.6670 (m-80) cc_final: 0.6345 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0931
  time to fit residues: 26.0924
Evaluate side-chains
  154 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 58 optimal weight:    0.3980
   chunk 30 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 67 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 193 GLN
F 227 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.155027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133203 restraints weight = 16143.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.135819 restraints weight = 11939.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.137270 restraints weight = 8984.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.138013 restraints weight = 5810.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.138537 restraints weight = 5316.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.5860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9048  Z= 0.150
  Angle     :  0.624   6.871  12452  Z= 0.323
  Chirality :  0.045   0.238   1439
  Planarity :  0.004   0.046   1422
  Dihedral  : 14.984 146.590   1741
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.27), residues: 954
  helix:  0.37 (0.28), residues: 349
  sheet: -1.48 (0.36), residues: 198
  loop : -0.80 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 406 
 TYR   0.025   0.002   TYR A 291 
 PHE   0.012   0.001   PHE F 143 
 TRP   0.047   0.003   TRP A 533 
 HIS   0.004   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9048)
  covalent geometry    : angle       0.62425 (12452)
  hydrogen bonds       : bond        0.04023 (  349)
  hydrogen bonds       : angle       4.73860 (  980)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7488 (ttpt) cc_final: 0.7228 (ttpt)
REVERT: A  303 LEU cc_start: 0.9062 (mp) cc_final: 0.8811 (mp)
REVERT: A  324 GLU cc_start: 0.7810 (pp20) cc_final: 0.7482 (tm-30)
REVERT: A  381 GLU cc_start: 0.8283 (tt0) cc_final: 0.7946 (mm-30)
REVERT: A  385 LYS cc_start: 0.8563 (tmtt) cc_final: 0.8027 (mmtp)
REVERT: A  404 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8099 (mttt)
REVERT: A  568 LEU cc_start: 0.7973 (pt) cc_final: 0.7691 (pt)
REVERT: A  760 LYS cc_start: 0.8819 (tptp) cc_final: 0.8508 (mptt)
REVERT: A  861 SER cc_start: 0.8968 (p) cc_final: 0.8745 (p)
REVERT: F  147 ASP cc_start: 0.7891 (t70) cc_final: 0.7554 (t0)
REVERT: F  177 PHE cc_start: 0.6639 (m-80) cc_final: 0.6309 (m-80)
REVERT: F  285 THR cc_start: 0.7857 (p) cc_final: 0.7626 (p)
REVERT: F  290 CYS cc_start: 0.7975 (p) cc_final: 0.7766 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.0853
  time to fit residues: 23.8610
Evaluate side-chains
  143 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.0970
   chunk 23 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.5382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 227 ASN
F 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.152118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.130052 restraints weight = 16142.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.131400 restraints weight = 12100.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.133501 restraints weight = 9472.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.134221 restraints weight = 6545.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.134746 restraints weight = 6158.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.6183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9048  Z= 0.183
  Angle     :  0.667   8.173  12452  Z= 0.346
  Chirality :  0.046   0.241   1439
  Planarity :  0.005   0.048   1422
  Dihedral  : 14.988 147.976   1741
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.92 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.27), residues: 954
  helix:  0.09 (0.27), residues: 348
  sheet: -1.34 (0.37), residues: 195
  loop : -0.90 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 406 
 TYR   0.022   0.002   TYR A 291 
 PHE   0.014   0.002   PHE F 143 
 TRP   0.038   0.003   TRP A 533 
 HIS   0.004   0.001   HIS A 855 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 9048)
  covalent geometry    : angle       0.66714 (12452)
  hydrogen bonds       : bond        0.04411 (  349)
  hydrogen bonds       : angle       4.84353 (  980)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 GLU cc_start: 0.7804 (pp20) cc_final: 0.7500 (tm-30)
REVERT: A  381 GLU cc_start: 0.8357 (tt0) cc_final: 0.7965 (mm-30)
REVERT: A  385 LYS cc_start: 0.8541 (tmtt) cc_final: 0.7921 (mmtp)
REVERT: A  404 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8133 (mttt)
REVERT: A  515 TRP cc_start: 0.8437 (p90) cc_final: 0.7396 (p90)
REVERT: A  568 LEU cc_start: 0.7946 (pt) cc_final: 0.7659 (pt)
REVERT: A  625 VAL cc_start: 0.8511 (t) cc_final: 0.8305 (m)
REVERT: A  734 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7655 (mtt-85)
REVERT: A  760 LYS cc_start: 0.8795 (tptp) cc_final: 0.8501 (mptt)
REVERT: A  780 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8464 (mtpp)
REVERT: A  861 SER cc_start: 0.8976 (p) cc_final: 0.8513 (p)
REVERT: F   89 MET cc_start: 0.7178 (mmp) cc_final: 0.6364 (mmm)
REVERT: F  285 THR cc_start: 0.7956 (p) cc_final: 0.7686 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0870
  time to fit residues: 23.0108
Evaluate side-chains
  146 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 92 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 753 HIS
F 227 ASN
F 300 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.151993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.129864 restraints weight = 16114.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.130929 restraints weight = 11596.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.133153 restraints weight = 9478.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.133976 restraints weight = 6498.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.134711 restraints weight = 6572.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.6414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9048  Z= 0.184
  Angle     :  0.674   9.931  12452  Z= 0.349
  Chirality :  0.046   0.239   1439
  Planarity :  0.005   0.045   1422
  Dihedral  : 14.991 148.958   1741
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.92 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.27), residues: 954
  helix:  0.10 (0.28), residues: 347
  sheet: -1.36 (0.38), residues: 181
  loop : -0.99 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 309 
 TYR   0.021   0.002   TYR A 291 
 PHE   0.020   0.002   PHE F 312 
 TRP   0.036   0.003   TRP A 533 
 HIS   0.004   0.001   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 9048)
  covalent geometry    : angle       0.67421 (12452)
  hydrogen bonds       : bond        0.04365 (  349)
  hydrogen bonds       : angle       4.90116 (  980)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 GLU cc_start: 0.7792 (pp20) cc_final: 0.7496 (tm-30)
REVERT: A  381 GLU cc_start: 0.8362 (tt0) cc_final: 0.7994 (mm-30)
REVERT: A  385 LYS cc_start: 0.8560 (tmtt) cc_final: 0.7928 (mmtp)
REVERT: A  404 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8129 (mttt)
REVERT: A  515 TRP cc_start: 0.8466 (p90) cc_final: 0.7622 (p90)
REVERT: A  568 LEU cc_start: 0.7886 (pt) cc_final: 0.7524 (pt)
REVERT: A  734 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7542 (mtt-85)
REVERT: A  760 LYS cc_start: 0.8804 (tptp) cc_final: 0.8511 (mptt)
REVERT: A  780 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8495 (mtpp)
REVERT: A  861 SER cc_start: 0.8918 (p) cc_final: 0.8617 (p)
REVERT: F   89 MET cc_start: 0.7119 (mmp) cc_final: 0.6318 (mmm)
REVERT: F  119 TYR cc_start: 0.6028 (m-10) cc_final: 0.5795 (m-10)
REVERT: F  285 THR cc_start: 0.8012 (p) cc_final: 0.7732 (p)
REVERT: F  290 CYS cc_start: 0.8440 (p) cc_final: 0.8176 (p)
REVERT: F  312 PHE cc_start: 0.8150 (m-10) cc_final: 0.7935 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0894
  time to fit residues: 23.7995
Evaluate side-chains
  143 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0270
   chunk 89 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0040
   chunk 3 optimal weight:    0.0970
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.2448

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 HIS
F 227 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.157928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.136058 restraints weight = 15894.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.139007 restraints weight = 11283.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.140818 restraints weight = 8135.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.141070 restraints weight = 5482.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.141206 restraints weight = 5344.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.6519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9048  Z= 0.118
  Angle     :  0.612   6.724  12452  Z= 0.316
  Chirality :  0.044   0.225   1439
  Planarity :  0.005   0.048   1422
  Dihedral  : 15.001 150.555   1741
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.27), residues: 954
  helix:  0.21 (0.28), residues: 348
  sheet: -1.08 (0.38), residues: 181
  loop : -0.87 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 589 
 TYR   0.022   0.002   TYR A 291 
 PHE   0.023   0.001   PHE F 312 
 TRP   0.025   0.002   TRP F 310 
 HIS   0.003   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9048)
  covalent geometry    : angle       0.61153 (12452)
  hydrogen bonds       : bond        0.03822 (  349)
  hydrogen bonds       : angle       4.68454 (  980)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 GLU cc_start: 0.7788 (pp20) cc_final: 0.7516 (tm-30)
REVERT: A  381 GLU cc_start: 0.8246 (tt0) cc_final: 0.7917 (mm-30)
REVERT: A  385 LYS cc_start: 0.8467 (tmtt) cc_final: 0.7935 (mmtp)
REVERT: A  404 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8035 (mttt)
REVERT: A  473 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7956 (mt-10)
REVERT: A  515 TRP cc_start: 0.8261 (p90) cc_final: 0.7522 (p90)
REVERT: A  568 LEU cc_start: 0.7863 (pt) cc_final: 0.7498 (pt)
REVERT: A  734 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7569 (mtt-85)
REVERT: A  760 LYS cc_start: 0.8803 (tptp) cc_final: 0.8537 (mptt)
REVERT: A  780 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8529 (mtpp)
REVERT: F   89 MET cc_start: 0.7000 (mmp) cc_final: 0.6249 (mmm)
REVERT: F  119 TYR cc_start: 0.5739 (m-10) cc_final: 0.5503 (m-10)
REVERT: F  285 THR cc_start: 0.7814 (p) cc_final: 0.7552 (p)
REVERT: F  290 CYS cc_start: 0.8305 (p) cc_final: 0.8093 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1034
  time to fit residues: 26.1842
Evaluate side-chains
  143 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 27 optimal weight:    0.3980
   chunk 99 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 753 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.157395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.135669 restraints weight = 15810.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.135724 restraints weight = 11908.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.137925 restraints weight = 9694.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.140591 restraints weight = 6477.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.140460 restraints weight = 5384.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.6615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9048  Z= 0.127
  Angle     :  0.622   9.977  12452  Z= 0.319
  Chirality :  0.045   0.224   1439
  Planarity :  0.004   0.046   1422
  Dihedral  : 14.955 151.468   1741
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.11 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.27), residues: 954
  helix:  0.19 (0.27), residues: 348
  sheet: -1.12 (0.38), residues: 181
  loop : -0.83 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 606 
 TYR   0.029   0.002   TYR A 603 
 PHE   0.012   0.001   PHE F 143 
 TRP   0.027   0.003   TRP F 310 
 HIS   0.006   0.001   HIS A 753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9048)
  covalent geometry    : angle       0.62226 (12452)
  hydrogen bonds       : bond        0.03753 (  349)
  hydrogen bonds       : angle       4.62557 (  980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1431.84 seconds
wall clock time: 25 minutes 50.16 seconds (1550.16 seconds total)