Starting phenix.real_space_refine
on Wed Aug  5 11:04:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nhd_49409/08_2026/9nhd_49409.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nhd_49409/08_2026/9nhd_49409.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nhd_49409/08_2026/9nhd_49409.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nhd_49409/08_2026/9nhd_49409.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nhd_49409/08_2026/9nhd_49409.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nhd_49409/08_2026/9nhd_49409.map"
  }
  resolution = 4.1
  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=   0.000 sd=   0.042
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      48      5.49       5
     Mg      1      5.21       5
     S      39      5.16       5
     C    5712      2.51       5
     N    1582      2.21       5
     O    1853      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9235
  Number of models: 1
  Model: ""
    Number of chains: 6
    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: 518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 518
          Classifications: {'RNA': 24}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 14, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 2, 'rna3p': 21}
    Chain: "C"
      Number of atoms: 501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 501
          Classifications: {'RNA': 24}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 2, 'rna3p': 21}
    Chain: "E"
      Number of atoms: 373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 373
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 3, 'TRANS': 41}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1901
          Classifications: {'peptide': 236}
          Link IDs: {'PTRANS': 13, 'TRANS': 222}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.17, per 1000 atoms: 0.23
  Number of scatterers: 9235
  At special positions: 0
  Unit cell: (105.56, 95.55, 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      48     15.00
     Mg      1     11.99
     O    1853      8.00
     N    1582      7.00
     C    5712      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: 0.76
  Conformation dependent library (CDL) restraints added in 261.7 milliseconds
  

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1930

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 11 sheets defined
      40.0% alpha, 16.6% beta
      20 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 0.90
  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
      removed outlier: 3.536A  pdb=" N   VAL A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    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: 3.856A  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: 3.654A  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 516 through 522
      removed outlier: 3.612A  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 516 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: 4.105A  pdb=" N   VAL A 616 " --> pdb=" O   LYS A 612 " (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 746 through 752
    Processing helix  chain 'A' and resid 754 through 767
    Processing helix  chain 'A' and resid 842 through 855
    Processing helix  chain 'A' and resid 867 through 880
    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 'E' and resid 114 through 119
      removed outlier: 3.606A  pdb=" N   LYS E 118 " --> pdb=" O   ASP E 114 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 131 through 135
    Processing helix  chain 'E' and resid 137 through 145
      removed outlier: 4.221A  pdb=" N   LYS E 143 " --> pdb=" O   LYS E 139 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR E 144 " --> pdb=" O   GLU E 140 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 110
      removed outlier: 3.765A  pdb=" N   GLU F  93 " --> pdb=" O   MET F  89 " (cutoff:3.500A)
      removed outlier: 4.109A  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: 5.074A  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 277
      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: 3.784A  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: 3.846A  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: 7.785A  pdb=" N   ILE A 776 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
      removed outlier: 5.828A  pdb=" N   ILE A 737 " --> pdb=" O   ILE A 776 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL A 778 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 6.783A  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: 6.370A  pdb=" N   ILE A 595 " --> pdb=" O   GLN A 623 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   VAL A 625 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 6.107A  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: 4.622A  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: 7.788A  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)

    323 hydrogen bonds defined for protein.
    921 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      48 hydrogen bonds
      96 hydrogen bond angles
      0 basepair planarities
      20 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 1.72

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2583
        1.34 -     1.46: 1957
        1.46 -     1.58: 4826
        1.58 -     1.70: 94
        1.70 -     1.82: 61
  Bond restraints: 9521
  Sorted by residual:
  bond pdb=" C4    C C  10 "
       pdb=" N4    C C  10 "
    ideal  model  delta    sigma   weight residual
    1.335  1.298  0.037 9.00e-03 1.23e+04 1.71e+01
  bond pdb=" C4    C C  11 "
       pdb=" N4    C C  11 "
    ideal  model  delta    sigma   weight residual
    1.335  1.298  0.037 9.00e-03 1.23e+04 1.69e+01
  bond pdb=" C4    C C  17 "
       pdb=" N4    C C  17 "
    ideal  model  delta    sigma   weight residual
    1.335  1.299  0.036 9.00e-03 1.23e+04 1.58e+01
  bond pdb=" CZ  ARG A 812 "
       pdb=" NH2 ARG A 812 "
    ideal  model  delta    sigma   weight residual
    1.330  1.282  0.048 1.30e-02 5.92e+03 1.35e+01
  bond pdb=" CA  PRO F 213 "
       pdb=" C   PRO F 213 "
    ideal  model  delta    sigma   weight residual
    1.514  1.533 -0.019 5.50e-03 3.31e+04 1.22e+01
  ... (remaining 9516 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 12032
        2.23 -     4.45: 957
        4.45 -     6.68: 103
        6.68 -     8.91: 11
        8.91 -    11.13: 4
  Bond angle restraints: 13107
  Sorted by residual:
  angle pdb=" C3'   G B   5 "
        pdb=" O3'   G B   5 "
        pdb=" P     U B   6 "
      ideal   model   delta    sigma   weight residual
     119.70  108.57   11.13 1.20e+00 6.94e-01 8.61e+01
  angle pdb=" N6    A C  12 "
        pdb=" C6    A C  12 "
        pdb=" N1    A C  12 "
      ideal   model   delta    sigma   weight residual
     118.60  113.47    5.13 6.00e-01 2.78e+00 7.30e+01
  angle pdb=" C3'   G B   3 "
        pdb=" O3'   G B   3 "
        pdb=" P     A B   4 "
      ideal   model   delta    sigma   weight residual
     119.70  111.18    8.52 1.20e+00 6.94e-01 5.05e+01
  angle pdb=" C5    A C  18 "
        pdb=" C6    A C  18 "
        pdb=" N1    A C  18 "
      ideal   model   delta    sigma   weight residual
     117.70  121.18   -3.48 5.00e-01 4.00e+00 4.86e+01
  angle pdb=" O2    C C  17 "
        pdb=" C2    C C  17 "
        pdb=" N3    C C  17 "
      ideal   model   delta    sigma   weight residual
     121.90  117.26    4.64 7.00e-01 2.04e+00 4.39e+01
  ... (remaining 13102 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.86: 5498
       27.86 -    55.73: 256
       55.73 -    83.59: 71
       83.59 -   111.45: 5
      111.45 -   139.32: 1
  Dihedral angle restraints: 5831
    sinusoidal: 2843
      harmonic: 2988
  Sorted by residual:
  dihedral pdb=" CA  ILE F 198 "
           pdb=" C   ILE F 198 "
           pdb=" N   ILE F 199 "
           pdb=" CA  ILE F 199 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.17   27.83     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" C5'   U B   6 "
           pdb=" C4'   U B   6 "
           pdb=" C3'   U B   6 "
           pdb=" O3'   U B   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  112.03   34.97     1      8.00e+00 1.56e-02 2.71e+01
  dihedral pdb=" C3'   U B   6 "
           pdb=" C4'   U B   6 "
           pdb=" O4'   U B   6 "
           pdb=" C1'   U B   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   30.64  -32.64     1      8.00e+00 1.56e-02 2.37e+01
  ... (remaining 5828 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1332
       0.105 -    0.211: 162
       0.211 -    0.316: 15
       0.316 -    0.422: 4
       0.422 -    0.527: 2
  Chirality restraints: 1515
  Sorted by residual:
  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    2.94   -0.53 2.00e-01 2.50e+01 6.94e+00
  chirality pdb=" P     G B   3 "
            pdb=" OP1   G B   3 "
            pdb=" OP2   G B   3 "
            pdb=" O5'   G B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.87   -0.46 2.00e-01 2.50e+01 5.27e+00
  chirality pdb=" P     A B   4 "
            pdb=" OP1   A B   4 "
            pdb=" OP2   A B   4 "
            pdb=" O5'   A B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.80   -0.39 2.00e-01 2.50e+01 3.78e+00
  ... (remaining 1512 not shown)

  Planarity restraints: 1490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C  18 "    0.144 2.00e-02 2.50e+03   6.32e-02 1.10e+02
        pdb=" N9    A C  18 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8    A C  18 "   -0.091 2.00e-02 2.50e+03
        pdb=" N7    A C  18 "   -0.036 2.00e-02 2.50e+03
        pdb=" C5    A C  18 "    0.006 2.00e-02 2.50e+03
        pdb=" C6    A C  18 "    0.032 2.00e-02 2.50e+03
        pdb=" N6    A C  18 "    0.085 2.00e-02 2.50e+03
        pdb=" N1    A C  18 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A C  18 "   -0.045 2.00e-02 2.50e+03
        pdb=" N3    A C  18 "   -0.048 2.00e-02 2.50e+03
        pdb=" C4    A C  18 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 245 "    0.095 2.00e-02 2.50e+03   5.86e-02 6.88e+01
        pdb=" CG  TYR A 245 "    0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 245 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 245 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 245 "   -0.030 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 245 "   -0.051 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 245 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 245 "    0.094 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 199 "    0.094 2.00e-02 2.50e+03   5.56e-02 6.19e+01
        pdb=" CG  TYR A 199 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 199 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 199 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 199 "   -0.042 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 199 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 199 "   -0.015 2.00e-02 2.50e+03
        pdb=" OH  TYR A 199 "    0.095 2.00e-02 2.50e+03
  ... (remaining 1487 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 45
        2.51 -     3.11: 6753
        3.11 -     3.71: 14782
        3.71 -     4.30: 19700
        4.30 -     4.90: 31547
  Nonbonded interactions: 72827
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 612 "
            pdb=" OD2 ASP F 283 "
     model   vdw
     1.916 3.120
  nonbonded pdb=" O3'   G C  15 "
            pdb="MG    MG C 101 "
     model   vdw
     2.041 2.170
  nonbonded pdb=" OP1   U C  16 "
            pdb="MG    MG C 101 "
     model   vdw
     2.111 2.170
  nonbonded pdb=" OD1 ASP A 740 "
            pdb="MG    MG C 101 "
     model   vdw
     2.157 2.170
  nonbonded pdb=" OG1 THR A 516 "
            pdb=" OG  SER A 861 "
     model   vdw
     2.244 3.040
  ... (remaining 72822 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.970
  Find NCS groups from input model:        0.040
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
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      :  0.007   0.048   9521  Z= 0.462
  Angle     :  1.212  11.134  13107  Z= 0.827
  Chirality :  0.070   0.527   1515
  Planarity :  0.010   0.108   1490
  Dihedral  : 16.584 139.317   3901
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.73 %
    Favored  : 97.16 %
  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: -1.21 (0.25), residues: 995
  helix: -0.27 (0.27), residues: 340
  sheet: -0.80 (0.39), residues: 169
  loop : -1.11 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 301 
 TYR   0.096   0.013   TYR A 271 
 PHE   0.071   0.008   PHE A 898 
 TRP   0.071   0.006   TRP A 477 
 HIS   0.010   0.002   HIS A 874 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00748 /  0.46 ( 9521)
  covalent geometry    : angle       1.21245 /  0.83 (13107)
  hydrogen bonds       : bond        0.20048 / 13.21 (  365)
  hydrogen bonds       : angle       7.07153 /  4.77 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 LYS cc_start: 0.9074 (ttpt) cc_final: 0.8791 (mttp)
REVERT: A  265 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6959 (tm-30)
REVERT: A  267 MET cc_start: 0.8447 (mmm) cc_final: 0.7830 (mmm)
REVERT: A  381 GLU cc_start: 0.8429 (tt0) cc_final: 0.7736 (mt-10)
REVERT: A  412 LEU cc_start: 0.8027 (mm) cc_final: 0.7734 (mm)
REVERT: A  563 MET cc_start: 0.6960 (mtt) cc_final: 0.6704 (mtt)
REVERT: A  641 LYS cc_start: 0.7355 (mtpt) cc_final: 0.7146 (tppt)
REVERT: A  871 GLN cc_start: 0.7796 (mm110) cc_final: 0.7516 (mm110)
REVERT: A  897 TYR cc_start: 0.7623 (p90) cc_final: 0.7181 (p90)
REVERT: F  215 MET cc_start: 0.7039 (mpp) cc_final: 0.5993 (mpp)
REVERT: F  303 THR cc_start: 0.8681 (p) cc_final: 0.8406 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0838
  time to fit residues: 23.0516
Evaluate side-chains
  149 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 249 GLN
A 297 GLN
A 388 ASN
F 197 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.123708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.103302 restraints weight = 20800.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.106682 restraints weight = 11450.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.107419 restraints weight = 7126.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.107740 restraints weight = 5812.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.107838 restraints weight = 5349.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9521  Z= 0.166
  Angle     :  0.646   7.479  13107  Z= 0.351
  Chirality :  0.045   0.253   1515
  Planarity :  0.005   0.069   1490
  Dihedral  : 15.267 141.775   1846
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.82 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.97 (0.27), residues: 995
  helix: -0.06 (0.27), residues: 358
  sheet: -0.72 (0.39), residues: 192
  loop : -0.97 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 606 
 TYR   0.018   0.002   TYR A 872 
 PHE   0.016   0.002   PHE A 464 
 TRP   0.010   0.002   TRP A 288 
 HIS   0.010   0.002   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.17 ( 9521)
  covalent geometry    : angle       0.64614 /  0.35 (13107)
  hydrogen bonds       : bond        0.05982 /  3.93 (  365)
  hydrogen bonds       : angle       5.44515 /  3.76 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 LYS cc_start: 0.9145 (ttpt) cc_final: 0.8850 (mttp)
REVERT: A  265 GLN cc_start: 0.7060 (tm-30) cc_final: 0.6748 (tm-30)
REVERT: A  267 MET cc_start: 0.8397 (mmm) cc_final: 0.7937 (mmm)
REVERT: A  412 LEU cc_start: 0.7808 (mm) cc_final: 0.7576 (mm)
REVERT: A  665 MET cc_start: 0.7377 (ttm) cc_final: 0.7129 (ttm)
REVERT: F  101 GLN cc_start: 0.7900 (pm20) cc_final: 0.7685 (pm20)
REVERT: F  215 MET cc_start: 0.6827 (mpp) cc_final: 0.5778 (mpp)
REVERT: F  303 THR cc_start: 0.8728 (p) cc_final: 0.8412 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 178
  average time/residue: 0.0846
  time to fit residues: 22.1225
Evaluate side-chains
  137 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 75 optimal weight:   20.0000
   chunk 60 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0980
   chunk 61 optimal weight:    0.8980
   chunk 81 optimal weight:    9.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 388 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.121895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.101789 restraints weight = 20811.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.104644 restraints weight = 11441.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.105738 restraints weight = 7014.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.106075 restraints weight = 5613.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.106355 restraints weight = 5347.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9521  Z= 0.178
  Angle     :  0.626   6.830  13107  Z= 0.335
  Chirality :  0.045   0.254   1515
  Planarity :  0.005   0.056   1490
  Dihedral  : 15.211 143.485   1846
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.69 %
    Favored  : 95.20 %
  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: -0.98 (0.27), residues: 995
  helix: -0.06 (0.27), residues: 359
  sheet: -0.83 (0.39), residues: 190
  loop : -0.94 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 223 
 TYR   0.032   0.002   TYR A 697 
 PHE   0.018   0.002   PHE F 267 
 TRP   0.024   0.002   TRP A 533 
 HIS   0.007   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.18 ( 9521)
  covalent geometry    : angle       0.62593 /  0.33 (13107)
  hydrogen bonds       : bond        0.05444 /  3.55 (  365)
  hydrogen bonds       : angle       5.21065 /  3.57 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 169
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 LYS cc_start: 0.9193 (ttpt) cc_final: 0.8904 (mttp)
REVERT: A  265 GLN cc_start: 0.7103 (tm-30) cc_final: 0.5996 (tm-30)
REVERT: A  412 LEU cc_start: 0.7805 (mm) cc_final: 0.7524 (mm)
REVERT: A  603 TYR cc_start: 0.7394 (m-10) cc_final: 0.6974 (m-10)
REVERT: F  101 GLN cc_start: 0.7892 (pm20) cc_final: 0.7641 (pm20)
REVERT: F  215 MET cc_start: 0.6922 (mpp) cc_final: 0.5903 (mpp)
REVERT: F  303 THR cc_start: 0.8724 (p) cc_final: 0.8402 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0846
  time to fit residues: 20.9231
Evaluate side-chains
  132 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   overall best weight:    1.0786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.123029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.102755 restraints weight = 21025.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105292 restraints weight = 11482.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.106407 restraints weight = 7372.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.106633 restraints weight = 5990.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.106970 restraints weight = 5662.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9521  Z= 0.133
  Angle     :  0.592   6.265  13107  Z= 0.312
  Chirality :  0.044   0.255   1515
  Planarity :  0.004   0.048   1490
  Dihedral  : 15.208 144.048   1846
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.18 %
    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: 995
  helix:  0.13 (0.27), residues: 359
  sheet: -0.89 (0.38), residues: 196
  loop : -0.88 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 865 
 TYR   0.020   0.002   TYR A 872 
 PHE   0.019   0.002   PHE F 267 
 TRP   0.018   0.002   TRP A 533 
 HIS   0.009   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 ( 9521)
  covalent geometry    : angle       0.59182 /  0.31 (13107)
  hydrogen bonds       : bond        0.04651 /  3.05 (  365)
  hydrogen bonds       : angle       4.96390 /  3.40 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6591 (tm-30)
REVERT: A  636 MET cc_start: 0.6540 (ppp) cc_final: 0.5138 (mtt)
REVERT: A  698 SER cc_start: 0.9105 (p) cc_final: 0.8887 (p)
REVERT: F  215 MET cc_start: 0.6953 (mpp) cc_final: 0.5914 (mpp)
REVERT: F  303 THR cc_start: 0.8685 (p) cc_final: 0.8361 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0848
  time to fit residues: 21.0327
Evaluate side-chains
  134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 77 optimal weight:    9.9990
   chunk 91 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 871 GLN
F  91 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.123045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.103072 restraints weight = 20767.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.106059 restraints weight = 11183.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.106885 restraints weight = 6968.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.107369 restraints weight = 5638.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.107696 restraints weight = 5242.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9521  Z= 0.141
  Angle     :  0.596   6.557  13107  Z= 0.314
  Chirality :  0.043   0.254   1515
  Planarity :  0.004   0.047   1490
  Dihedral  : 15.202 144.468   1846
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  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: -0.83 (0.27), residues: 995
  helix:  0.12 (0.27), residues: 359
  sheet: -0.88 (0.38), residues: 196
  loop : -0.84 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 865 
 TYR   0.019   0.002   TYR A 872 
 PHE   0.016   0.002   PHE F 267 
 TRP   0.015   0.002   TRP A 533 
 HIS   0.005   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 9521)
  covalent geometry    : angle       0.59551 /  0.31 (13107)
  hydrogen bonds       : bond        0.04543 /  3.02 (  365)
  hydrogen bonds       : angle       4.89024 /  3.36 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6661 (tm-30)
REVERT: A  636 MET cc_start: 0.6479 (ppp) cc_final: 0.5176 (mtt)
REVERT: F  101 GLN cc_start: 0.8013 (pm20) cc_final: 0.7659 (pm20)
REVERT: F  215 MET cc_start: 0.6997 (mpp) cc_final: 0.5949 (mpp)
REVERT: F  303 THR cc_start: 0.8698 (p) cc_final: 0.8377 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0802
  time to fit residues: 19.6352
Evaluate side-chains
  137 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 76 optimal weight:   10.9990
   chunk 32 optimal weight:    0.6980
   chunk 100 optimal weight:    5.9990
   chunk 98 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 73 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    2.9388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.117742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.098151 restraints weight = 21356.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.100507 restraints weight = 11622.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.101426 restraints weight = 7455.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.101992 restraints weight = 6244.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.102467 restraints weight = 5699.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9521  Z= 0.266
  Angle     :  0.722   7.809  13107  Z= 0.380
  Chirality :  0.048   0.261   1515
  Planarity :  0.005   0.050   1490
  Dihedral  : 15.233 145.690   1846
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.73 %
    Favored  : 97.16 %
  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: -1.25 (0.26), residues: 995
  helix: -0.23 (0.26), residues: 359
  sheet: -1.36 (0.36), residues: 195
  loop : -0.92 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 562 
 TYR   0.029   0.003   TYR A 872 
 PHE   0.020   0.003   PHE A 787 
 TRP   0.022   0.003   TRP A 533 
 HIS   0.005   0.002   HIS E 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00597 /  0.27 ( 9521)
  covalent geometry    : angle       0.72153 /  0.38 (13107)
  hydrogen bonds       : bond        0.05804 /  3.88 (  365)
  hydrogen bonds       : angle       5.21892 /  3.59 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7201 (tm-30) cc_final: 0.6095 (tm-30)
REVERT: A  455 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8080 (mm-30)
REVERT: A  603 TYR cc_start: 0.7405 (m-10) cc_final: 0.7180 (m-10)
REVERT: A  837 ASP cc_start: 0.8702 (t0) cc_final: 0.8472 (t0)
REVERT: F  101 GLN cc_start: 0.8253 (pm20) cc_final: 0.8045 (pm20)
REVERT: F  215 MET cc_start: 0.7149 (mpp) cc_final: 0.6109 (mpp)
REVERT: F  303 THR cc_start: 0.8844 (p) cc_final: 0.8546 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0881
  time to fit residues: 20.4045
Evaluate side-chains
  124 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 83 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0170
   overall best weight:    0.6220

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.122525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.102548 restraints weight = 20742.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.105595 restraints weight = 11051.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.106703 restraints weight = 6788.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107053 restraints weight = 5308.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.107298 restraints weight = 4915.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9521  Z= 0.123
  Angle     :  0.607   8.118  13107  Z= 0.317
  Chirality :  0.043   0.256   1515
  Planarity :  0.004   0.051   1490
  Dihedral  : 15.307 145.247   1846
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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: -0.78 (0.27), residues: 995
  helix:  0.05 (0.27), residues: 360
  sheet: -0.63 (0.39), residues: 188
  loop : -0.80 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 269 
 TYR   0.016   0.002   TYR A 696 
 PHE   0.020   0.001   PHE A 337 
 TRP   0.023   0.002   TRP F 310 
 HIS   0.002   0.001   HIS F 154 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 ( 9521)
  covalent geometry    : angle       0.60747 /  0.32 (13107)
  hydrogen bonds       : bond        0.04398 /  2.94 (  365)
  hydrogen bonds       : angle       4.85557 /  3.32 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7122 (tm-30) cc_final: 0.6347 (tm-30)
REVERT: A  267 MET cc_start: 0.8118 (mmm) cc_final: 0.7401 (mmm)
REVERT: A  563 MET cc_start: 0.6652 (mtt) cc_final: 0.6351 (mtt)
REVERT: A  636 MET cc_start: 0.6558 (ppp) cc_final: 0.4982 (mtt)
REVERT: A  871 GLN cc_start: 0.8036 (mm110) cc_final: 0.7827 (mm-40)
REVERT: F  101 GLN cc_start: 0.8244 (pm20) cc_final: 0.8026 (pm20)
REVERT: F  181 MET cc_start: 0.8177 (mmm) cc_final: 0.7932 (mmm)
REVERT: F  215 MET cc_start: 0.6991 (mpp) cc_final: 0.5966 (mpp)
REVERT: F  303 THR cc_start: 0.8602 (p) cc_final: 0.8302 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0888
  time to fit residues: 21.0871
Evaluate side-chains
  127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 13 optimal weight:    0.0970
   chunk 46 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 39 optimal weight:    0.4980
   chunk 20 optimal weight:    0.0370
   chunk 51 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.4056

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.123901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.103875 restraints weight = 20557.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.106927 restraints weight = 11032.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.107743 restraints weight = 6754.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.108286 restraints weight = 5506.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108591 restraints weight = 5067.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9521  Z= 0.118
  Angle     :  0.599   8.664  13107  Z= 0.312
  Chirality :  0.043   0.251   1515
  Planarity :  0.004   0.048   1490
  Dihedral  : 15.246 145.208   1846
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  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: -0.64 (0.27), residues: 995
  helix:  0.17 (0.27), residues: 360
  sheet: -0.48 (0.40), residues: 191
  loop : -0.77 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 292 
 TYR   0.022   0.001   TYR A 603 
 PHE   0.022   0.001   PHE A 337 
 TRP   0.017   0.002   TRP A 515 
 HIS   0.002   0.001   HIS A 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 9521)
  covalent geometry    : angle       0.59929 /  0.31 (13107)
  hydrogen bonds       : bond        0.04142 /  2.77 (  365)
  hydrogen bonds       : angle       4.73938 /  3.24 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6521 (tm-30)
REVERT: A  269 ARG cc_start: 0.8345 (tpp-160) cc_final: 0.8098 (tpp80)
REVERT: A  372 MET cc_start: 0.7776 (ttt) cc_final: 0.7509 (ttt)
REVERT: A  636 MET cc_start: 0.6220 (ppp) cc_final: 0.5006 (mtt)
REVERT: F  101 GLN cc_start: 0.8314 (pm20) cc_final: 0.8095 (pm20)
REVERT: F  215 MET cc_start: 0.6937 (mpp) cc_final: 0.5965 (mpp)
REVERT: F  303 THR cc_start: 0.8485 (p) cc_final: 0.8137 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0900
  time to fit residues: 22.0416
Evaluate side-chains
  133 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0370
   chunk 33 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0000
   chunk 86 optimal weight:    6.9990
   chunk 3 optimal weight:    0.0670
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.4200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 265 GLN
A 459 ASN
E 121 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.124940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.104898 restraints weight = 20331.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.107867 restraints weight = 10881.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.109120 restraints weight = 6752.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.109580 restraints weight = 5208.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.109797 restraints weight = 4788.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9521  Z= 0.115
  Angle     :  0.594   8.649  13107  Z= 0.309
  Chirality :  0.043   0.250   1515
  Planarity :  0.004   0.051   1490
  Dihedral  : 15.219 145.362   1846
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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: -0.62 (0.27), residues: 995
  helix:  0.20 (0.27), residues: 360
  sheet: -0.45 (0.40), residues: 191
  loop : -0.80 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 292 
 TYR   0.024   0.001   TYR A 603 
 PHE   0.023   0.001   PHE A 337 
 TRP   0.024   0.002   TRP A 362 
 HIS   0.002   0.001   HIS A 753 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 ( 9521)
  covalent geometry    : angle       0.59369 /  0.31 (13107)
  hydrogen bonds       : bond        0.04044 /  2.74 (  365)
  hydrogen bonds       : angle       4.67781 /  3.19 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.7260 (tm130) cc_final: 0.6783 (tm-30)
REVERT: A  269 ARG cc_start: 0.8358 (tpp-160) cc_final: 0.8131 (tpp80)
REVERT: A  563 MET cc_start: 0.6955 (mtt) cc_final: 0.6604 (mtt)
REVERT: A  636 MET cc_start: 0.6146 (ppp) cc_final: 0.4843 (mtt)
REVERT: F  101 GLN cc_start: 0.8277 (pm20) cc_final: 0.7970 (pm20)
REVERT: F  167 MET cc_start: 0.8358 (tpt) cc_final: 0.7871 (tpt)
REVERT: F  215 MET cc_start: 0.6880 (mpp) cc_final: 0.5906 (mpp)
REVERT: F  303 THR cc_start: 0.8483 (p) cc_final: 0.8158 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.0820
  time to fit residues: 19.6876
Evaluate side-chains
  137 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 75 optimal weight:   20.0000
   chunk 98 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   chunk 94 optimal weight:    0.6980
   chunk 68 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 712 HIS
A 871 GLN
E 121 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.121433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.101752 restraints weight = 20843.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.104751 restraints weight = 11019.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.105845 restraints weight = 6789.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.106170 restraints weight = 5373.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.106306 restraints weight = 4944.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9521  Z= 0.174
  Angle     :  0.630   7.520  13107  Z= 0.333
  Chirality :  0.045   0.251   1515
  Planarity :  0.004   0.048   1490
  Dihedral  : 15.169 146.179   1846
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  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: -0.79 (0.27), residues: 995
  helix:  0.16 (0.27), residues: 359
  sheet: -0.77 (0.39), residues: 195
  loop : -0.87 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 292 
 TYR   0.025   0.002   TYR A 603 
 PHE   0.022   0.002   PHE A 337 
 TRP   0.017   0.002   TRP A 533 
 HIS   0.004   0.001   HIS A 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.17 ( 9521)
  covalent geometry    : angle       0.63050 /  0.33 (13107)
  hydrogen bonds       : bond        0.04595 /  3.09 (  365)
  hydrogen bonds       : angle       4.79057 /  3.29 ( 1017)

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

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

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1990 Ramachandran restraints generated.
    995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  269 ARG cc_start: 0.8472 (tpp-160) cc_final: 0.8227 (tpp80)
REVERT: A  455 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8044 (mm-30)
REVERT: A  563 MET cc_start: 0.7025 (mtt) cc_final: 0.6620 (mtt)
REVERT: A  636 MET cc_start: 0.6514 (ppp) cc_final: 0.5115 (mtt)
REVERT: F  101 GLN cc_start: 0.8321 (pm20) cc_final: 0.8083 (pm20)
REVERT: F  303 THR cc_start: 0.8621 (p) cc_final: 0.8330 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0849
  time to fit residues: 20.3398
Evaluate side-chains
  127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    0.0970
   chunk 89 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 99 optimal weight:    0.0070
   chunk 52 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.9800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 886 ASN
E 121 HIS
F  91 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.122938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.102489 restraints weight = 20564.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.105498 restraints weight = 11349.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.106479 restraints weight = 6679.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.106714 restraints weight = 5802.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.106975 restraints weight = 5481.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9521  Z= 0.134
  Angle     :  0.609   8.046  13107  Z= 0.319
  Chirality :  0.044   0.250   1515
  Planarity :  0.004   0.047   1490
  Dihedral  : 15.200 146.183   1846
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  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: -0.75 (0.27), residues: 995
  helix:  0.20 (0.27), residues: 359
  sheet: -0.73 (0.39), residues: 195
  loop : -0.84 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 606 
 TYR   0.022   0.002   TYR A 603 
 PHE   0.011   0.001   PHE A 548 
 TRP   0.055   0.003   TRP A 533 
 HIS   0.003   0.001   HIS A 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.13 ( 9521)
  covalent geometry    : angle       0.60890 /  0.32 (13107)
  hydrogen bonds       : bond        0.04159 /  2.79 (  365)
  hydrogen bonds       : angle       4.70695 /  3.21 ( 1017)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1391.50 seconds
wall clock time: 25 minutes 1.99 seconds (1501.99 seconds total)