Starting phenix.real_space_refine
on Thu Jul  2 15:35:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nhe_49410/07_2026/9nhe_49410.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nhe_49410/07_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_49410/07_2026/9nhe_49410.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nhe_49410/07_2026/9nhe_49410.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nhe_49410/07_2026/9nhe_49410.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nhe_49410/07_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-dev-6108/lib/python3.11/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: 1.80, per 1000 atoms: 0.21
  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: 0.73
  Conformation dependent library (CDL) restraints added in 200.2 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: 0.81
  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: 1.11

  Time building geometry restraints manager: 0.92 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=" C4    C B  11 "
       pdb=" N4    C B  11 "
    ideal  model  delta    sigma   weight residual
    1.335  1.296  0.039 9.00e-03 1.23e+04 1.87e+01
  bond pdb=" C4    C C  17 "
       pdb=" N4    C C  17 "
    ideal  model  delta    sigma   weight residual
    1.335  1.297  0.038 9.00e-03 1.23e+04 1.77e+01
  bond pdb=" C2    G C  15 "
       pdb=" N2    G C  15 "
    ideal  model  delta    sigma   weight residual
    1.341  1.299  0.042 1.00e-02 1.00e+04 1.74e+01
  bond pdb=" C2    G B   5 "
       pdb=" N2    G B   5 "
    ideal  model  delta    sigma   weight residual
    1.341  1.300  0.041 1.00e-02 1.00e+04 1.72e+01
  bond pdb=" C4    C C  23 "
       pdb=" N4    C C  23 "
    ideal  model  delta    sigma   weight residual
    1.335  1.298  0.037 9.00e-03 1.23e+04 1.71e+01
  ... (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=" N6    A B  12 "
        pdb=" C6    A B  12 "
        pdb=" N1    A B  12 "
      ideal   model   delta    sigma   weight residual
     118.60  113.09    5.51 6.00e-01 2.78e+00 8.42e+01
  angle pdb=" N6    A B  10 "
        pdb=" C6    A B  10 "
        pdb=" N1    A B  10 "
      ideal   model   delta    sigma   weight residual
     118.60  113.43    5.17 6.00e-01 2.78e+00 7.44e+01
  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=" C5    A B  13 "
        pdb=" C6    A B  13 "
        pdb=" N1    A B  13 "
      ideal   model   delta    sigma   weight residual
     117.70  121.43   -3.73 5.00e-01 4.00e+00 5.56e+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
  ... (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:             2.040
  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:                    0.030
  Process input model:                     8.730
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
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= 0.619
  Angle     :  1.492  11.663  12452  Z= 1.089
  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/Z
  covalent geometry    : bond        0.00941 /  0.62 ( 9048)
  covalent geometry    : angle       1.49249 /  1.09 (12452)
  hydrogen bonds       : bond        0.20558 / 14.50 (  349)
  hydrogen bonds       : angle       7.54556 /  5.05 (  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  : 0.194 
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: 0.1022
  time to fit residues: 39.2062
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  : 0.307 
-------------------------------------------------------------------------------
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...
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 172 HIS
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 746 GLN
F 197 ASN
F 231 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.164541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.142413 restraints weight = 16161.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.145285 restraints weight = 11584.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.146860 restraints weight = 8669.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.147716 restraints weight = 5626.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.147959 restraints weight = 5213.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9048  Z= 0.184
  Angle     :  0.748   6.670  12452  Z= 0.412
  Chirality :  0.050   0.263   1439
  Planarity :  0.007   0.152   1422
  Dihedral  : 15.857 140.779   1741
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  4.93 %
    Favored  : 94.39 %
  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: -1.01 (0.27), residues: 954
  helix: -0.00 (0.28), residues: 340
  sheet: -0.93 (0.39), residues: 185
  loop : -0.99 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 373 
 TYR   0.029   0.003   TYR A 291 
 PHE   0.024   0.003   PHE F 177 
 TRP   0.013   0.002   TRP A 533 
 HIS   0.009   0.002   HIS A 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.18 ( 9048)
  covalent geometry    : angle       0.74805 /  0.41 (12452)
  hydrogen bonds       : bond        0.06229 /  4.16 (  349)
  hydrogen bonds       : angle       5.52736 /  3.71 (  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
  220 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 214
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  381 GLU cc_start: 0.8513 (tt0) cc_final: 0.8300 (tp30)
REVERT: A  385 LYS cc_start: 0.8865 (tmtt) cc_final: 0.8589 (mttm)
REVERT: A  568 LEU cc_start: 0.7409 (pt) cc_final: 0.7148 (pt)
REVERT: A  578 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7086 (mp0)
REVERT: A  734 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6952 (mtt-85)
REVERT: A  760 LYS cc_start: 0.8770 (tptp) cc_final: 0.8499 (mptt)
REVERT: A  780 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8656 (mtpp)
REVERT: F   89 MET cc_start: 0.6962 (mmp) cc_final: 0.6515 (mmm)
REVERT: F  105 LYS cc_start: 0.7699 (pptt) cc_final: 0.7458 (mttp)
REVERT: F  119 TYR cc_start: 0.5756 (m-80) cc_final: 0.5155 (m-10)
REVERT: F  177 PHE cc_start: 0.6672 (m-80) cc_final: 0.6151 (m-80)
REVERT: F  201 TYR cc_start: 0.7635 (t80) cc_final: 0.6979 (t80)
  outliers start: 6
  outliers final: 1
  residues processed: 217
  average time/residue: 0.0798
  time to fit residues: 23.6776
Evaluate side-chains
  159 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 5 optimal weight:    0.1980
   chunk 40 optimal weight:    0.7980
   chunk 77 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 459 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.159231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.136642 restraints weight = 15936.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.137956 restraints weight = 11946.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.140050 restraints weight = 9183.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.141011 restraints weight = 6169.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.141375 restraints weight = 6269.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   9048  Z= 0.199
  Angle     :  0.695   8.120  12452  Z= 0.378
  Chirality :  0.048   0.236   1439
  Planarity :  0.005   0.055   1422
  Dihedral  : 15.649 141.538   1741
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  4.81 %
    Favored  : 94.73 %
  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: -0.98 (0.27), residues: 954
  helix:  0.18 (0.28), residues: 344
  sheet: -1.23 (0.38), residues: 186
  loop : -0.94 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 792 
 TYR   0.030   0.002   TYR A 291 
 PHE   0.021   0.002   PHE F 267 
 TRP   0.016   0.002   TRP A 533 
 HIS   0.004   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.20 ( 9048)
  covalent geometry    : angle       0.69477 /  0.38 (12452)
  hydrogen bonds       : bond        0.05714 /  3.85 (  349)
  hydrogen bonds       : angle       5.22666 /  3.48 (  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
  209 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 205
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.7943 (tt) cc_final: 0.7590 (tt)
REVERT: A  292 LYS cc_start: 0.7658 (ttpt) cc_final: 0.7119 (ttmt)
REVERT: A  381 GLU cc_start: 0.8529 (tt0) cc_final: 0.8269 (tp30)
REVERT: A  385 LYS cc_start: 0.8698 (tmtt) cc_final: 0.8385 (mttm)
REVERT: A  542 ARG cc_start: 0.7754 (tpt90) cc_final: 0.7385 (tpt90)
REVERT: A  578 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6812 (mp0)
REVERT: A  760 LYS cc_start: 0.8809 (tptp) cc_final: 0.8536 (mptt)
REVERT: F  119 TYR cc_start: 0.6051 (m-80) cc_final: 0.5227 (m-80)
REVERT: F  177 PHE cc_start: 0.6967 (m-80) cc_final: 0.6589 (m-80)
REVERT: F  201 TYR cc_start: 0.7675 (t80) cc_final: 0.6781 (t80)
REVERT: F  254 THR cc_start: 0.8919 (p) cc_final: 0.8643 (p)
REVERT: F  285 THR cc_start: 0.7998 (p) cc_final: 0.7750 (p)
  outliers start: 4
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0852
  time to fit residues: 23.7629
Evaluate side-chains
  152 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
A 602 ASN
F 227 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.156974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.134748 restraints weight = 16535.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.136514 restraints weight = 12665.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.138116 restraints weight = 9973.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.139408 restraints weight = 6582.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.139249 restraints weight = 6278.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   9048  Z= 0.203
  Angle     :  0.691   8.794  12452  Z= 0.373
  Chirality :  0.048   0.241   1439
  Planarity :  0.005   0.051   1422
  Dihedral  : 15.521 142.903   1741
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.55 %
    Favored  : 96.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.07 (0.27), residues: 954
  helix:  0.15 (0.27), residues: 343
  sheet: -1.40 (0.37), residues: 188
  loop : -0.97 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 520 
 TYR   0.034   0.002   TYR A 696 
 PHE   0.032   0.002   PHE F 253 
 TRP   0.020   0.002   TRP A 533 
 HIS   0.006   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00455 /  0.20 ( 9048)
  covalent geometry    : angle       0.69135 /  0.37 (12452)
  hydrogen bonds       : bond        0.05257 /  3.59 (  349)
  hydrogen bonds       : angle       5.16186 /  3.46 (  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
  197 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.320 
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: 0.7558 (ttpt) cc_final: 0.7100 (ttmt)
REVERT: A  303 LEU cc_start: 0.8762 (mp) cc_final: 0.8514 (mp)
REVERT: A  381 GLU cc_start: 0.8449 (tt0) cc_final: 0.8195 (tp30)
REVERT: A  385 LYS cc_start: 0.8720 (tmtt) cc_final: 0.8347 (mmtp)
REVERT: A  760 LYS cc_start: 0.8780 (tptp) cc_final: 0.8538 (mptt)
REVERT: F   89 MET cc_start: 0.7239 (mmp) cc_final: 0.6765 (mmm)
REVERT: F  119 TYR cc_start: 0.6093 (m-80) cc_final: 0.5594 (m-10)
REVERT: F  177 PHE cc_start: 0.7010 (m-80) cc_final: 0.6714 (m-80)
REVERT: F  201 TYR cc_start: 0.7709 (t80) cc_final: 0.7241 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0784
  time to fit residues: 21.4466
Evaluate side-chains
  148 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0770
   chunk 49 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.7340

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4090 r_free = 0.4090 target = 0.160003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.138482 restraints weight = 15993.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.138559 restraints weight = 12215.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.140952 restraints weight = 9781.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.142449 restraints weight = 6601.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.142901 restraints weight = 5826.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9048  Z= 0.137
  Angle     :  0.645   7.066  12452  Z= 0.344
  Chirality :  0.047   0.237   1439
  Planarity :  0.005   0.053   1422
  Dihedral  : 15.442 143.228   1741
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.06 %
    Favored  : 97.71 %
  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: -0.90 (0.27), residues: 954
  helix:  0.20 (0.28), residues: 346
  sheet: -1.25 (0.36), residues: 188
  loop : -0.82 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 606 
 TYR   0.037   0.002   TYR A 291 
 PHE   0.019   0.001   PHE A 337 
 TRP   0.014   0.002   TRP F 310 
 HIS   0.003   0.001   HIS A 855 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00300 /  0.14 ( 9048)
  covalent geometry    : angle       0.64540 /  0.34 (12452)
  hydrogen bonds       : bond        0.04744 /  3.29 (  349)
  hydrogen bonds       : angle       4.97744 /  3.31 (  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
  208 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 206
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7445 (ttpt) cc_final: 0.7065 (ttmt)
REVERT: A  303 LEU cc_start: 0.8695 (mp) cc_final: 0.8453 (mp)
REVERT: A  381 GLU cc_start: 0.8417 (tt0) cc_final: 0.8174 (tp30)
REVERT: A  385 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8285 (mttm)
REVERT: A  578 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7141 (mp0)
REVERT: A  760 LYS cc_start: 0.8716 (tptp) cc_final: 0.8507 (mptt)
REVERT: F  119 TYR cc_start: 0.5919 (m-80) cc_final: 0.5337 (m-80)
REVERT: F  177 PHE cc_start: 0.7044 (m-80) cc_final: 0.6604 (m-80)
REVERT: F  201 TYR cc_start: 0.7585 (t80) cc_final: 0.6910 (t80)
REVERT: F  285 THR cc_start: 0.7868 (p) cc_final: 0.7662 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 207
  average time/residue: 0.0784
  time to fit residues: 22.4289
Evaluate side-chains
  151 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0970
   chunk 86 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 75 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
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 = 0.4090 r_free = 0.4090 target = 0.160486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.138433 restraints weight = 16122.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.140232 restraints weight = 12129.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.142024 restraints weight = 9648.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.143183 restraints weight = 6397.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.143505 restraints weight = 6002.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.4775

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= 0.131
  Angle     :  0.619   6.649  12452  Z= 0.328
  Chirality :  0.045   0.235   1439
  Planarity :  0.004   0.046   1422
  Dihedral  : 15.336 143.740   1741
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.06 %
    Favored  : 97.71 %
  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:  0.28 (0.27), residues: 348
  sheet: -1.20 (0.35), residues: 194
  loop : -0.86 (0.32), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 792 
 TYR   0.034   0.002   TYR A 291 
 PHE   0.011   0.001   PHE F 267 
 TRP   0.010   0.001   TRP A 533 
 HIS   0.002   0.001   HIS A 712 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 9048)
  covalent geometry    : angle       0.61855 /  0.33 (12452)
  hydrogen bonds       : bond        0.04430 /  3.08 (  349)
  hydrogen bonds       : angle       4.87864 /  3.26 (  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: 2
    poor density    : 197
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 LYS cc_start: 0.7492 (ttpt) cc_final: 0.7078 (ttmt)
REVERT: A  381 GLU cc_start: 0.8410 (tt0) cc_final: 0.8141 (tp30)
REVERT: A  385 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8336 (mmtp)
REVERT: A  578 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7197 (mp0)
REVERT: A  760 LYS cc_start: 0.8790 (tptp) cc_final: 0.8500 (mptt)
REVERT: F   89 MET cc_start: 0.7111 (mmt) cc_final: 0.6661 (mmm)
REVERT: F  177 PHE cc_start: 0.7030 (m-80) cc_final: 0.6552 (m-80)
REVERT: F  285 THR cc_start: 0.7798 (p) cc_final: 0.7558 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0756
  time to fit residues: 20.8899
Evaluate side-chains
  160 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
A 874 HIS
F 227 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.156419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.135387 restraints weight = 16451.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.136165 restraints weight = 12217.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.137886 restraints weight = 10045.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.139596 restraints weight = 6763.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.139592 restraints weight = 5508.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9048  Z= 0.170
  Angle     :  0.684  14.579  12452  Z= 0.357
  Chirality :  0.047   0.238   1439
  Planarity :  0.004   0.045   1422
  Dihedral  : 15.273 143.961   1741
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.29 %
    Favored  : 97.59 %
  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:  0.22 (0.28), residues: 346
  sheet: -1.28 (0.36), residues: 194
  loop : -0.90 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 269 
 TYR   0.042   0.002   TYR A 291 
 PHE   0.031   0.002   PHE A 272 
 TRP   0.024   0.002   TRP A 477 
 HIS   0.003   0.001   HIS A 712 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.17 ( 9048)
  covalent geometry    : angle       0.68416 /  0.36 (12452)
  hydrogen bonds       : bond        0.04633 /  3.18 (  349)
  hydrogen bonds       : angle       4.99801 /  3.35 (  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
  198 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 LEU cc_start: 0.7507 (mm) cc_final: 0.7223 (tt)
REVERT: A  231 ARG cc_start: 0.7110 (mtm110) cc_final: 0.5974 (mtp-110)
REVERT: A  381 GLU cc_start: 0.8408 (tt0) cc_final: 0.8135 (tp30)
REVERT: A  385 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8086 (mmtp)
REVERT: A  439 MET cc_start: 0.7077 (ttp) cc_final: 0.6780 (tmm)
REVERT: A  568 LEU cc_start: 0.7728 (pt) cc_final: 0.7410 (pt)
REVERT: A  760 LYS cc_start: 0.8756 (tptp) cc_final: 0.8511 (mptt)
REVERT: A  896 LEU cc_start: 0.8374 (mm) cc_final: 0.8040 (mp)
REVERT: F   89 MET cc_start: 0.7040 (mmt) cc_final: 0.6560 (mmm)
REVERT: F  147 ASP cc_start: 0.7697 (t70) cc_final: 0.7408 (t0)
REVERT: F  177 PHE cc_start: 0.6954 (m-80) cc_final: 0.6435 (m-80)
REVERT: F  285 THR cc_start: 0.7832 (p) cc_final: 0.7604 (p)
REVERT: F  290 CYS cc_start: 0.7684 (p) cc_final: 0.7430 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 198
  average time/residue: 0.0914
  time to fit residues: 25.4060
Evaluate side-chains
  141 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 23 optimal weight:    0.0470
   chunk 94 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0980
   chunk 63 optimal weight:    0.8980
   chunk 7 optimal weight:    0.1980
   chunk 85 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.4478

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 GLN
A 265 GLN
F 227 ASN
F 257 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.160084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.137999 restraints weight = 16068.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.141011 restraints weight = 11829.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.142766 restraints weight = 8378.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.143415 restraints weight = 5618.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.143820 restraints weight = 5583.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.5248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9048  Z= 0.127
  Angle     :  0.646  12.688  12452  Z= 0.336
  Chirality :  0.045   0.230   1439
  Planarity :  0.005   0.080   1422
  Dihedral  : 15.237 144.005   1741
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.72 %
    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: -0.82 (0.27), residues: 954
  helix:  0.20 (0.27), residues: 348
  sheet: -1.11 (0.36), residues: 195
  loop : -0.76 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 406 
 TYR   0.028   0.002   TYR A 291 
 PHE   0.014   0.001   PHE F 143 
 TRP   0.013   0.002   TRP F 310 
 HIS   0.004   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 ( 9048)
  covalent geometry    : angle       0.64616 /  0.34 (12452)
  hydrogen bonds       : bond        0.04160 /  2.88 (  349)
  hydrogen bonds       : angle       4.76589 /  3.20 (  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
  201 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 LEU cc_start: 0.7484 (mm) cc_final: 0.7132 (tt)
REVERT: A  231 ARG cc_start: 0.7131 (mtm110) cc_final: 0.6247 (mtp-110)
REVERT: A  324 GLU cc_start: 0.7855 (pp20) cc_final: 0.7330 (tm-30)
REVERT: A  381 GLU cc_start: 0.8339 (tt0) cc_final: 0.7980 (mm-30)
REVERT: A  385 LYS cc_start: 0.8537 (tmtt) cc_final: 0.8040 (mmtp)
REVERT: A  568 LEU cc_start: 0.7797 (pt) cc_final: 0.7478 (pt)
REVERT: A  603 TYR cc_start: 0.6438 (m-10) cc_final: 0.6186 (m-10)
REVERT: A  760 LYS cc_start: 0.8710 (tptp) cc_final: 0.8479 (mptt)
REVERT: F   89 MET cc_start: 0.6993 (mmt) cc_final: 0.6673 (tpp)
REVERT: F  177 PHE cc_start: 0.6945 (m-80) cc_final: 0.6421 (m-80)
REVERT: F  195 LEU cc_start: 0.8156 (mm) cc_final: 0.7901 (mm)
REVERT: F  250 THR cc_start: 0.7359 (t) cc_final: 0.7112 (t)
REVERT: F  285 THR cc_start: 0.7803 (p) cc_final: 0.7555 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0972
  time to fit residues: 27.3094
Evaluate side-chains
  161 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 92 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 76 optimal weight:    9.9990
   overall best weight:    1.7184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 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 = 0.4015 r_free = 0.4015 target = 0.154054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.132155 restraints weight = 16301.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.134013 restraints weight = 11953.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.136120 restraints weight = 8852.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.136523 restraints weight = 6061.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.136713 restraints weight = 5821.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.5564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9048  Z= 0.207
  Angle     :  0.719   8.904  12452  Z= 0.379
  Chirality :  0.048   0.241   1439
  Planarity :  0.005   0.047   1422
  Dihedral  : 15.218 144.706   1741
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.69 %
    Favored  : 99.20 %
  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: -1.19 (0.27), residues: 954
  helix:  0.03 (0.27), residues: 346
  sheet: -1.70 (0.35), residues: 201
  loop : -0.85 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 606 
 TYR   0.032   0.002   TYR A 291 
 PHE   0.019   0.002   PHE F 143 
 TRP   0.051   0.003   TRP A 533 
 HIS   0.005   0.001   HIS A 172 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00469 /  0.21 ( 9048)
  covalent geometry    : angle       0.71875 /  0.38 (12452)
  hydrogen bonds       : bond        0.04806 /  3.33 (  349)
  hydrogen bonds       : angle       4.97138 /  3.37 (  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
  195 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ARG cc_start: 0.7263 (mtm110) cc_final: 0.6359 (mtp-110)
REVERT: A  324 GLU cc_start: 0.7882 (pp20) cc_final: 0.7505 (tm-30)
REVERT: A  381 GLU cc_start: 0.8342 (tt0) cc_final: 0.8004 (mm-30)
REVERT: A  385 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8020 (mttm)
REVERT: A  406 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7728 (ptm160)
REVERT: A  439 MET cc_start: 0.7479 (tmm) cc_final: 0.7239 (ttm)
REVERT: A  515 TRP cc_start: 0.8401 (p90) cc_final: 0.7960 (p90)
REVERT: A  542 ARG cc_start: 0.7655 (tpt90) cc_final: 0.7392 (tpt90)
REVERT: A  568 LEU cc_start: 0.7877 (pt) cc_final: 0.7527 (pt)
REVERT: A  760 LYS cc_start: 0.8814 (tptp) cc_final: 0.8514 (mptt)
REVERT: F  177 PHE cc_start: 0.6955 (m-80) cc_final: 0.6453 (m-80)
REVERT: F  285 THR cc_start: 0.7877 (p) cc_final: 0.7594 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0920
  time to fit residues: 25.0228
Evaluate side-chains
  147 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.4051 r_free = 0.4051 target = 0.157179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.135324 restraints weight = 16134.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.136794 restraints weight = 11742.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.138973 restraints weight = 8988.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.139830 restraints weight = 6210.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.140327 restraints weight = 5676.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.5673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9048  Z= 0.143
  Angle     :  0.656   9.857  12452  Z= 0.346
  Chirality :  0.046   0.234   1439
  Planarity :  0.004   0.043   1422
  Dihedral  : 15.166 145.041   1741
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.23 %
    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: -1.04 (0.27), residues: 954
  helix:  0.12 (0.27), residues: 347
  sheet: -1.53 (0.34), residues: 200
  loop : -0.79 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 606 
 TYR   0.026   0.002   TYR A 291 
 PHE   0.012   0.001   PHE F 143 
 TRP   0.039   0.002   TRP A 533 
 HIS   0.002   0.001   HIS A 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 9048)
  covalent geometry    : angle       0.65608 /  0.35 (12452)
  hydrogen bonds       : bond        0.04224 /  2.94 (  349)
  hydrogen bonds       : angle       4.80417 /  3.23 (  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
  189 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  231 ARG cc_start: 0.7311 (mtm110) cc_final: 0.6397 (mtp-110)
REVERT: A  267 MET cc_start: 0.7848 (mmm) cc_final: 0.7529 (mmm)
REVERT: A  324 GLU cc_start: 0.7966 (pp20) cc_final: 0.7633 (tm-30)
REVERT: A  381 GLU cc_start: 0.8377 (tt0) cc_final: 0.7969 (mm-30)
REVERT: A  385 LYS cc_start: 0.8548 (tmtt) cc_final: 0.8018 (mmtp)
REVERT: A  406 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.7760 (ptm160)
REVERT: A  515 TRP cc_start: 0.8315 (p90) cc_final: 0.7714 (p90)
REVERT: A  568 LEU cc_start: 0.7988 (pt) cc_final: 0.7694 (pt)
REVERT: A  760 LYS cc_start: 0.8791 (tptp) cc_final: 0.8511 (mptt)
REVERT: A  861 SER cc_start: 0.8822 (p) cc_final: 0.8534 (p)
REVERT: F  177 PHE cc_start: 0.6907 (m-80) cc_final: 0.6387 (m-80)
REVERT: F  285 THR cc_start: 0.7792 (p) cc_final: 0.7516 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0997
  time to fit residues: 26.3580
Evaluate side-chains
  151 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
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:    0.0570
   chunk 44 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 227 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.158093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.136640 restraints weight = 15994.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.137988 restraints weight = 11611.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.140201 restraints weight = 9124.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.140600 restraints weight = 6245.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.141008 restraints weight = 6256.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.5725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9048  Z= 0.133
  Angle     :  0.653   8.924  12452  Z= 0.341
  Chirality :  0.046   0.232   1439
  Planarity :  0.005   0.114   1422
  Dihedral  : 15.138 145.596   1741
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  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: -0.95 (0.27), residues: 954
  helix:  0.19 (0.28), residues: 347
  sheet: -1.34 (0.35), residues: 198
  loop : -0.82 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 406 
 TYR   0.030   0.002   TYR A 603 
 PHE   0.013   0.001   PHE F 143 
 TRP   0.033   0.002   TRP A 533 
 HIS   0.002   0.001   HIS A 855 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 9048)
  covalent geometry    : angle       0.65288 /  0.34 (12452)
  hydrogen bonds       : bond        0.04019 /  2.82 (  349)
  hydrogen bonds       : angle       4.75572 /  3.19 (  980)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1315.59 seconds
wall clock time: 23 minutes 38.20 seconds (1418.20 seconds total)