Starting phenix.real_space_refine
on Thu Mar  5 22:35:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p7w_20271/03_2026/6p7w_20271.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p7w_20271/03_2026/6p7w_20271.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/6p7w_20271/03_2026/6p7w_20271.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p7w_20271/03_2026/6p7w_20271.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p7w_20271/03_2026/6p7w_20271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p7w_20271/03_2026/6p7w_20271.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=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    8370      2.51       5
     N    2126      2.21       5
     O    2308      1.98       5
     H   12936      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 25800
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "E"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 1589
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 4, 'TRANS': 89}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 6464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 6464
          Classifications: {'peptide': 387}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 373}
    Chain: "D"
      Number of atoms: 2059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 2059
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 7, 'TRANS': 118}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 7977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 7977
          Classifications: {'peptide': 476}
          Link IDs: {'PTRANS': 14, 'TRANS': 461}
          Chain breaks: 6
    Chain: "A"
      Number of atoms: 7711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 459, 7711
          Classifications: {'peptide': 459}
          Link IDs: {'PTRANS': 14, 'TRANS': 444}
          Chain breaks: 6
  Time building chain proxies: 4.70, per 1000 atoms: 0.18
  Number of scatterers: 25800
  At special positions: 0
  Unit cell: (93.324, 135.744, 127.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     O    2308      8.00
     N    2126      7.00
     C    8370      6.00
     H   12936      1.00
    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: 2.48
  Conformation dependent library (CDL) restraints added in 907.5 milliseconds
  

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3008

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 5 sheets defined
      67.8% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'E' and resid 4 through 10
    Processing helix  chain 'E' and resid 12 through 32
      removed outlier: 3.573A  pdb=" N   ALA E  16 " --> pdb=" O   PRO E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 57
    Processing helix  chain 'E' and resid 59 through 63
    Processing helix  chain 'E' and resid 64 through 76
    Processing helix  chain 'E' and resid 81 through 101
      removed outlier: 4.138A  pdb=" N   PHE E 101 " --> pdb=" O   LYS E  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 9
    Processing helix  chain 'C' and resid 11 through 22
      removed outlier: 3.882A  pdb=" N   ARG C  15 " --> pdb=" O   PRO C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 64
    Processing helix  chain 'C' and resid 72 through 83
    Processing helix  chain 'C' and resid 86 through 100
    Processing helix  chain 'C' and resid 132 through 140
    Processing helix  chain 'C' and resid 157 through 170
    Processing helix  chain 'C' and resid 189 through 195
    Processing helix  chain 'C' and resid 196 through 198
      No H-bonds generated for 'chain 'C' and resid 196 through 198'
    Processing helix  chain 'C' and resid 211 through 217
    Processing helix  chain 'C' and resid 234 through 239
    Processing helix  chain 'C' and resid 303 through 309
    Processing helix  chain 'C' and resid 327 through 345
    Processing helix  chain 'C' and resid 367 through 371
    Processing helix  chain 'D' and resid 22 through 27
    Processing helix  chain 'D' and resid 29 through 35
    Processing helix  chain 'D' and resid 71 through 85
    Processing helix  chain 'D' and resid 95 through 101
    Processing helix  chain 'D' and resid 105 through 112
    Processing helix  chain 'D' and resid 115 through 130
      removed outlier: 3.716A  pdb=" N   LEU D 119 " --> pdb=" O   ASP D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 131 through 148
      removed outlier: 3.825A  pdb=" N   LEU D 135 " --> pdb=" O   ILE D 131 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 156
      removed outlier: 4.019A  pdb=" N   ILE D 154 " --> pdb=" O   THR D 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 81
    Processing helix  chain 'B' and resid 100 through 105
    Processing helix  chain 'B' and resid 118 through 133
    Processing helix  chain 'B' and resid 134 through 141
    Processing helix  chain 'B' and resid 145 through 162
    Processing helix  chain 'B' and resid 181 through 200
    Processing helix  chain 'B' and resid 202 through 210
      removed outlier: 3.594A  pdb=" N   ILE B 206 " --> pdb=" O   PRO B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 218
      removed outlier: 3.763A  pdb=" N   GLU B 216 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 256
    Processing helix  chain 'B' and resid 261 through 272
      removed outlier: 3.660A  pdb=" N   GLN B 265 " --> pdb=" O   VAL B 261 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ASN B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 278
    Processing helix  chain 'B' and resid 279 through 298
      removed outlier: 3.673A  pdb=" N   GLY B 298 " --> pdb=" O   ALA B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 333
    Processing helix  chain 'B' and resid 373 through 389
    Processing helix  chain 'B' and resid 394 through 413
    Processing helix  chain 'B' and resid 418 through 447
    Processing helix  chain 'B' and resid 451 through 473
      Proline residue:  B 459  - end of helix
    Processing helix  chain 'B' and resid 475 through 480
      removed outlier: 3.597A  pdb=" N   THR B 479 " --> pdb=" O   TYR B 475 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR B 480 " --> pdb=" O   PHE B 476 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 475 through 480'
    Processing helix  chain 'B' and resid 481 through 502
      removed outlier: 3.639A  pdb=" N   VAL B 485 " --> pdb=" O   HIS B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 522
    Processing helix  chain 'B' and resid 525 through 548
    Processing helix  chain 'B' and resid 560 through 578
      removed outlier: 4.545A  pdb=" N   GLU B 578 " --> pdb=" O   LYS B 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 618
    Processing helix  chain 'A' and resid 63 through 81
    Processing helix  chain 'A' and resid 118 through 133
    Processing helix  chain 'A' and resid 134 through 141
    Processing helix  chain 'A' and resid 145 through 162
    Processing helix  chain 'A' and resid 181 through 200
    Processing helix  chain 'A' and resid 202 through 210
      removed outlier: 3.584A  pdb=" N   ILE A 206 " --> pdb=" O   PRO A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 218
    Processing helix  chain 'A' and resid 232 through 256
      removed outlier: 3.655A  pdb=" N   ARG A 252 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   PHE A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   THR A 256 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 272
      removed outlier: 3.599A  pdb=" N   GLN A 265 " --> pdb=" O   VAL A 261 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ASN A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 297
    Processing helix  chain 'A' and resid 309 through 333
    Processing helix  chain 'A' and resid 373 through 389
    Processing helix  chain 'A' and resid 394 through 413
    Processing helix  chain 'A' and resid 418 through 447
    Processing helix  chain 'A' and resid 451 through 473
      Proline residue:  A 459  - end of helix
    Processing helix  chain 'A' and resid 475 through 480
      removed outlier: 3.533A  pdb=" N   THR A 479 " --> pdb=" O   TYR A 475 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   THR A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 475 through 480'
    Processing helix  chain 'A' and resid 481 through 502
      removed outlier: 3.640A  pdb=" N   VAL A 485 " --> pdb=" O   HIS A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 522
      removed outlier: 3.601A  pdb=" N   PHE A 522 " --> pdb=" O   LEU A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 548
    Processing helix  chain 'A' and resid 560 through 578
      removed outlier: 4.307A  pdb=" N   GLU A 578 " --> pdb=" O   LYS A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 618
    Processing sheet with id=AA1, first strand: chain 'C' and resid 105 through 111
      removed outlier: 3.601A  pdb=" N   VAL C 129 " --> pdb=" O   ILE C 119 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 148 through 151
      removed outlier: 4.242A  pdb=" N   LEU C 207 " --> pdb=" O   GLU C 242 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 276 through 277
      removed outlier: 7.107A  pdb=" N   ILE C 276 " --> pdb=" O   ILE C 299 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 363 through 366
    Processing sheet with id=AA5, first strand: chain 'D' and resid 16 through 21

    767 hydrogen bonds defined for protein.
    2265 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.12

  Time building geometry restraints manager: 3.47 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12905
        1.03 -     1.23: 80
        1.23 -     1.43: 5533
        1.43 -     1.62: 7488
        1.62 -     1.82: 89
  Bond restraints: 26095
  Sorted by residual:
  bond pdb=" C   ASP B 523 "
       pdb=" N   PRO B 524 "
    ideal  model  delta    sigma   weight residual
    1.334  1.393 -0.059 2.34e-02 1.83e+03 6.37e+00
  bond pdb=" CG1 ILE A 254 "
       pdb=" CD1 ILE A 254 "
    ideal  model  delta    sigma   weight residual
    1.513  1.443  0.070 3.90e-02 6.57e+02 3.26e+00
  bond pdb=" C   LYS B 305 "
       pdb=" N   ILE B 306 "
    ideal  model  delta    sigma   weight residual
    1.332  1.301  0.031 1.73e-02 3.34e+03 3.20e+00
  bond pdb=" CA  ILE A 212 "
       pdb=" C   ILE A 212 "
    ideal  model  delta    sigma   weight residual
    1.523  1.501  0.022 1.27e-02 6.20e+03 3.07e+00
  bond pdb=" C   ASP A 211 "
       pdb=" N   ILE A 212 "
    ideal  model  delta    sigma   weight residual
    1.332  1.310  0.022 1.36e-02 5.41e+03 2.71e+00
  ... (remaining 26090 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 45476
        1.91 -     3.83: 1532
        3.83 -     5.74: 163
        5.74 -     7.66: 22
        7.66 -     9.57: 6
  Bond angle restraints: 47199
  Sorted by residual:
  angle pdb=" N   VAL A 389 "
        pdb=" CA  VAL A 389 "
        pdb=" C   VAL A 389 "
      ideal   model   delta    sigma   weight residual
     111.58  116.32   -4.74 1.06e+00 8.90e-01 2.00e+01
  angle pdb=" N   LEU A 116 "
        pdb=" CA  LEU A 116 "
        pdb=" C   LEU A 116 "
      ideal   model   delta    sigma   weight residual
     110.80  119.93   -9.13 2.13e+00 2.20e-01 1.84e+01
  angle pdb=" N   ILE A 212 "
        pdb=" CA  ILE A 212 "
        pdb=" C   ILE A 212 "
      ideal   model   delta    sigma   weight residual
     109.34  101.63    7.71 2.08e+00 2.31e-01 1.37e+01
  angle pdb=" C   SER A 390 "
        pdb=" N   GLU A 391 "
        pdb=" CA  GLU A 391 "
      ideal   model   delta    sigma   weight residual
     121.80  130.64   -8.84 2.44e+00 1.68e-01 1.31e+01
  angle pdb=" C   ILE A 212 "
        pdb=" N   ASP A 213 "
        pdb=" CA  ASP A 213 "
      ideal   model   delta    sigma   weight residual
     120.28  115.08    5.20 1.44e+00 4.82e-01 1.30e+01
  ... (remaining 47194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 10515
       17.78 -    35.55: 1338
       35.55 -    53.33: 254
       53.33 -    71.11: 69
       71.11 -    88.88: 6
  Dihedral angle restraints: 12182
    sinusoidal: 6548
      harmonic: 5634
  Sorted by residual:
  dihedral pdb=" CA  TYR C 246 "
           pdb=" C   TYR C 246 "
           pdb=" N   THR C 247 "
           pdb=" CA  THR C 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.35   35.65     0      5.00e+00 4.00e-02 5.08e+01
  dihedral pdb=" CA  PHE B 110 "
           pdb=" C   PHE B 110 "
           pdb=" N   TYR B 111 "
           pdb=" CA  TYR B 111 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.57  -31.43     0      5.00e+00 4.00e-02 3.95e+01
  dihedral pdb=" CA  LEU A 220 "
           pdb=" C   LEU A 220 "
           pdb=" N   ASP A 221 "
           pdb=" CA  ASP A 221 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.81   31.19     0      5.00e+00 4.00e-02 3.89e+01
  ... (remaining 12179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1332
       0.041 -    0.082: 465
       0.082 -    0.124: 169
       0.124 -    0.165: 33
       0.165 -    0.206: 3
  Chirality restraints: 2002
  Sorted by residual:
  chirality pdb=" CA  LEU A 116 "
            pdb=" N   LEU A 116 "
            pdb=" C   LEU A 116 "
            pdb=" CB  LEU A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  ILE C  69 "
            pdb=" CA  ILE C  69 "
            pdb=" CG1 ILE C  69 "
            pdb=" CG2 ILE C  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" CG  LEU A 185 "
            pdb=" CB  LEU A 185 "
            pdb=" CD1 LEU A 185 "
            pdb=" CD2 LEU A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 6.85e-01
  ... (remaining 1999 not shown)

  Planarity restraints: 3687
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 211 "    0.039 2.00e-02 2.50e+03   7.74e-02 5.99e+01
        pdb=" C   ASP A 211 "   -0.134 2.00e-02 2.50e+03
        pdb=" O   ASP A 211 "    0.051 2.00e-02 2.50e+03
        pdb=" N   ILE A 212 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 532 "   -0.019 2.00e-02 2.50e+03   3.81e-02 1.45e+01
        pdb=" C   PHE A 532 "    0.066 2.00e-02 2.50e+03
        pdb=" O   PHE A 532 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   PHE A 533 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 535 "   -0.019 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   ASN A 535 "    0.065 2.00e-02 2.50e+03
        pdb=" O   ASN A 535 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU A 536 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 3684 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 3186
        2.24 -     2.83: 59708
        2.83 -     3.42: 67968
        3.42 -     4.01: 87619
        4.01 -     4.60: 136717
  Nonbonded interactions: 355198
  Sorted by model distance:
  nonbonded pdb=" O   SER D  12 "
            pdb=" H   GLY D  15 "
     model   vdw
     1.655 2.450
  nonbonded pdb=" O   VAL C 341 "
            pdb=" HG1 THR C 344 "
     model   vdw
     1.675 2.450
  nonbonded pdb=" OH  TYR C 338 "
            pdb=" HE  ARG C 368 "
     model   vdw
     1.677 2.450
  nonbonded pdb=" OD2 ASP D 105 "
            pdb=" H   ASP D 108 "
     model   vdw
     1.678 2.450
  nonbonded pdb=" OD1 ASN B 248 "
            pdb=" HE  ARG B 252 "
     model   vdw
     1.684 2.450
  ... (remaining 355193 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 62 through 220 or resid 231 through 618))
  selection = (chain 'B' and (resid 62 through 347 or (resid 372 and (name N or name CA or nam \ 
e C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name H \ 
B2 or name HB3 or name HD21 or name HD22)) or resid 373 through 618))
}

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:             2.100
  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:             0.140
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.840
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
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   0.070  13159  Z= 0.315
  Angle     :  0.942   9.125  17809  Z= 0.526
  Chirality :  0.049   0.206   2002
  Planarity :  0.006   0.077   2217
  Dihedral  : 15.401  88.882   4880
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 11.10 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  4.12 %
    Favored  : 95.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.77 (0.18), residues: 1504
  helix: -1.70 (0.14), residues: 969
  sheet: -3.94 (0.55), residues: 66
  loop : -3.77 (0.26), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 368 
 TYR   0.018   0.002   TYR C 338 
 PHE   0.040   0.003   PHE C 201 
 TRP   0.018   0.002   TRP A 378 
 HIS   0.011   0.002   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00698 (13159)
  covalent geometry    : angle       0.94229 (17809)
  hydrogen bonds       : bond        0.11811 (  767)
  hydrogen bonds       : angle       6.19154 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 210
  time to evaluate  : 0.706 
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: 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: 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: 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: symmetry clash
REVERT: E   48 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8944 (ptpp)
REVERT: E   89 GLN cc_start: 0.9263 (tt0) cc_final: 0.9050 (tp-100)
REVERT: D  132 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8999 (mmmm)
REVERT: B  378 TRP cc_start: 0.8580 (t-100) cc_final: 0.7932 (t-100)
REVERT: A   75 TYR cc_start: 0.8749 (t80) cc_final: 0.8519 (t80)
REVERT: A  319 MET cc_start: 0.8564 (ttm) cc_final: 0.8147 (ttm)
REVERT: A  330 ASP cc_start: 0.8722 (t70) cc_final: 0.8287 (t70)
REVERT: A  436 MET cc_start: 0.8895 (mmm) cc_final: 0.8555 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 211
  average time/residue: 0.2877
  time to fit residues: 85.5311
Evaluate side-chains
  140 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.2980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
E  57 HIS
C 107 GLN
C 160 ASN
C 264 GLN
C 336 ASN
C 362 ASN
D 116 GLN
** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 486 HIS
** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
A 454 GLN
A 576 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.086770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.065830 restraints weight = 169114.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.068640 restraints weight = 80393.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.070405 restraints weight = 50798.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.071424 restraints weight = 38040.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.072031 restraints weight = 32120.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13159  Z= 0.141
  Angle     :  0.635   6.116  17809  Z= 0.346
  Chirality :  0.039   0.178   2002
  Planarity :  0.005   0.058   2217
  Dihedral  :  6.629  61.709   1673
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.98 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.99 (0.20), residues: 1504
  helix: -0.12 (0.15), residues: 967
  sheet: -3.51 (0.56), residues: 71
  loop : -3.49 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 252 
 TYR   0.018   0.001   TYR A 111 
 PHE   0.024   0.001   PHE C 201 
 TRP   0.014   0.002   TRP A 323 
 HIS   0.010   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (13159)
  covalent geometry    : angle       0.63535 (17809)
  hydrogen bonds       : bond        0.04851 (  767)
  hydrogen bonds       : angle       5.12740 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.708 
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: 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: 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: 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: symmetry clash
REVERT: E   89 GLN cc_start: 0.9369 (tt0) cc_final: 0.9060 (tp-100)
REVERT: D  132 LYS cc_start: 0.9360 (mmtt) cc_final: 0.9011 (mmmm)
REVERT: B   69 PHE cc_start: 0.8064 (m-10) cc_final: 0.7708 (m-10)
REVERT: A  275 PHE cc_start: 0.9051 (t80) cc_final: 0.8776 (t80)
REVERT: A  330 ASP cc_start: 0.8814 (t70) cc_final: 0.8276 (t0)
REVERT: A  436 MET cc_start: 0.8813 (mmm) cc_final: 0.8535 (tpp)
REVERT: A  563 MET cc_start: 0.6533 (ppp) cc_final: 0.6289 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.2547
  time to fit residues: 70.0868
Evaluate side-chains
  144 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 131 optimal weight:    5.9990
   chunk 144 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 121 optimal weight:    2.9990
   chunk 135 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
C  75 ASN
C 216 ASN
C 264 GLN
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 HIS
B 292 HIS
** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.084910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.063676 restraints weight = 172251.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.066351 restraints weight = 84660.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.067982 restraints weight = 54904.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.068941 restraints weight = 42171.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.069418 restraints weight = 36108.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  13159  Z= 0.220
  Angle     :  0.659   6.045  17809  Z= 0.361
  Chirality :  0.039   0.192   2002
  Planarity :  0.005   0.058   2217
  Dihedral  :  6.204  47.453   1673
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.36 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.43 (0.21), residues: 1504
  helix:  0.29 (0.16), residues: 989
  sheet: -3.16 (0.55), residues: 80
  loop : -3.39 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 385 
 TYR   0.019   0.002   TYR A 111 
 PHE   0.024   0.002   PHE B 522 
 TRP   0.014   0.002   TRP B 378 
 HIS   0.010   0.002   HIS E  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (13159)
  covalent geometry    : angle       0.65852 (17809)
  hydrogen bonds       : bond        0.04760 (  767)
  hydrogen bonds       : angle       5.11402 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.693 
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: 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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  214 MET cc_start: 0.8008 (tmm) cc_final: 0.7181 (tmm)
REVERT: D  132 LYS cc_start: 0.9438 (mmtt) cc_final: 0.9103 (mmmm)
REVERT: B  400 MET cc_start: 0.9315 (mtp) cc_final: 0.9028 (mtp)
REVERT: A  319 MET cc_start: 0.8391 (ttm) cc_final: 0.7993 (ttm)
REVERT: A  330 ASP cc_start: 0.9140 (t70) cc_final: 0.8768 (t0)
REVERT: A  436 MET cc_start: 0.8821 (mmm) cc_final: 0.8421 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 169
  average time/residue: 0.2338
  time to fit residues: 58.4604
Evaluate side-chains
  137 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0030
   chunk 58 optimal weight:    1.9990
   chunk 143 optimal weight:   10.0000
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.8592

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

Flipped N/Q/H residues before XYZ refinement:
C 349 ASN
** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.085824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.064991 restraints weight = 168135.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.067778 restraints weight = 79484.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.069490 restraints weight = 50387.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.070491 restraints weight = 38119.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.071042 restraints weight = 32310.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13159  Z= 0.129
  Angle     :  0.565   6.075  17809  Z= 0.307
  Chirality :  0.038   0.157   2002
  Planarity :  0.004   0.058   2217
  Dihedral  :  5.865  48.544   1673
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.22), residues: 1504
  helix:  0.81 (0.16), residues: 988
  sheet: -3.09 (0.54), residues: 85
  loop : -3.30 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  30 
 TYR   0.020   0.001   TYR B 154 
 PHE   0.015   0.001   PHE C 201 
 TRP   0.014   0.001   TRP B  79 
 HIS   0.009   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (13159)
  covalent geometry    : angle       0.56526 (17809)
  hydrogen bonds       : bond        0.04290 (  767)
  hydrogen bonds       : angle       4.67195 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.735 
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: 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: 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: 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: symmetry clash
REVERT: D  132 LYS cc_start: 0.9374 (mmtt) cc_final: 0.9054 (mmmm)
REVERT: B  268 LEU cc_start: 0.9372 (mt) cc_final: 0.9171 (mt)
REVERT: B  276 LEU cc_start: 0.9382 (mt) cc_final: 0.8912 (mt)
REVERT: B  365 ASP cc_start: 0.8138 (t70) cc_final: 0.7862 (t70)
REVERT: B  400 MET cc_start: 0.9369 (mtp) cc_final: 0.9032 (mtp)
REVERT: B  411 THR cc_start: 0.7721 (m) cc_final: 0.7517 (p)
REVERT: A  319 MET cc_start: 0.8310 (ttm) cc_final: 0.7903 (ttm)
REVERT: A  330 ASP cc_start: 0.9198 (t70) cc_final: 0.8832 (t70)
REVERT: A  436 MET cc_start: 0.8777 (mmm) cc_final: 0.8319 (tpp)
REVERT: A  544 HIS cc_start: 0.8435 (m-70) cc_final: 0.8080 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.2319
  time to fit residues: 59.6378
Evaluate side-chains
  140 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 143 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 127 optimal weight:    6.9990
   chunk 122 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
E  57 HIS
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 433 ASN
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.085018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.063872 restraints weight = 168698.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.066664 restraints weight = 79729.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.068378 restraints weight = 50399.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.069418 restraints weight = 38094.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.069943 restraints weight = 32156.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  13159  Z= 0.186
  Angle     :  0.590   6.184  17809  Z= 0.323
  Chirality :  0.038   0.165   2002
  Planarity :  0.004   0.055   2217
  Dihedral  :  5.769  47.783   1673
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.57 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  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: -0.68 (0.22), residues: 1504
  helix:  0.90 (0.16), residues: 991
  sheet: -2.95 (0.58), residues: 80
  loop : -3.19 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 252 
 TYR   0.029   0.002   TYR A  75 
 PHE   0.022   0.001   PHE A 255 
 TRP   0.015   0.002   TRP A  79 
 HIS   0.009   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (13159)
  covalent geometry    : angle       0.59002 (17809)
  hydrogen bonds       : bond        0.04340 (  767)
  hydrogen bonds       : angle       4.75060 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.753 
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: 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: 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: 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: symmetry clash
REVERT: E   96 VAL cc_start: 0.8901 (p) cc_final: 0.8419 (p)
REVERT: D  132 LYS cc_start: 0.9424 (mmtt) cc_final: 0.9121 (mmmm)
REVERT: B  276 LEU cc_start: 0.9401 (mt) cc_final: 0.9109 (mt)
REVERT: B  365 ASP cc_start: 0.8431 (t70) cc_final: 0.8181 (t70)
REVERT: B  400 MET cc_start: 0.9449 (mtp) cc_final: 0.9248 (mtp)
REVERT: B  411 THR cc_start: 0.7888 (m) cc_final: 0.7665 (p)
REVERT: B  445 MET cc_start: 0.8307 (mtm) cc_final: 0.8105 (mtm)
REVERT: A  275 PHE cc_start: 0.8823 (t80) cc_final: 0.8607 (t80)
REVERT: A  319 MET cc_start: 0.8262 (ttm) cc_final: 0.7834 (ttm)
REVERT: A  330 ASP cc_start: 0.9242 (t70) cc_final: 0.8914 (t0)
REVERT: A  436 MET cc_start: 0.8791 (mmm) cc_final: 0.8363 (tpp)
REVERT: A  497 PHE cc_start: 0.8057 (t80) cc_final: 0.7851 (t80)
REVERT: A  544 HIS cc_start: 0.8423 (m-70) cc_final: 0.8052 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2329
  time to fit residues: 58.0768
Evaluate side-chains
  141 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 149 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
D  69 ASN
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 HIS
** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 128 HIS
A 156 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.083742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062895 restraints weight = 168814.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.065516 restraints weight = 81860.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.067104 restraints weight = 52584.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.068097 restraints weight = 40298.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.068576 restraints weight = 34153.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  13159  Z= 0.225
  Angle     :  0.622   6.540  17809  Z= 0.344
  Chirality :  0.039   0.248   2002
  Planarity :  0.004   0.055   2217
  Dihedral  :  5.733  46.749   1673
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.64 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.22), residues: 1504
  helix:  0.84 (0.16), residues: 990
  sheet: -3.19 (0.54), residues: 83
  loop : -3.19 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 208 
 TYR   0.016   0.002   TYR A  75 
 PHE   0.054   0.002   PHE A 255 
 TRP   0.013   0.001   TRP B  79 
 HIS   0.009   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (13159)
  covalent geometry    : angle       0.62234 (17809)
  hydrogen bonds       : bond        0.04638 (  767)
  hydrogen bonds       : angle       4.91138 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.707 
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: 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: 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: 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: symmetry clash
REVERT: E   96 VAL cc_start: 0.8868 (p) cc_final: 0.8350 (p)
REVERT: C   13 ASP cc_start: 0.8654 (p0) cc_final: 0.8312 (p0)
REVERT: D  132 LYS cc_start: 0.9446 (mmtt) cc_final: 0.9175 (mmmm)
REVERT: B  276 LEU cc_start: 0.9379 (mt) cc_final: 0.8772 (mt)
REVERT: B  411 THR cc_start: 0.7905 (m) cc_final: 0.7692 (p)
REVERT: A  275 PHE cc_start: 0.8832 (t80) cc_final: 0.8607 (t80)
REVERT: A  319 MET cc_start: 0.8205 (ttm) cc_final: 0.7823 (ttm)
REVERT: A  330 ASP cc_start: 0.9301 (t70) cc_final: 0.8981 (t0)
REVERT: A  436 MET cc_start: 0.8802 (mmm) cc_final: 0.8377 (tpp)
REVERT: A  544 HIS cc_start: 0.8414 (m-70) cc_final: 0.8007 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2344
  time to fit residues: 56.4777
Evaluate side-chains
  133 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 123 optimal weight:    2.9990
   chunk 118 optimal weight:    0.8980
   chunk 132 optimal weight:    9.9990
   chunk 84 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 142 optimal weight:    5.9990
   chunk 134 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0770
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
C  75 ASN
** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.085290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.064377 restraints weight = 165239.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.067094 restraints weight = 79364.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.068742 restraints weight = 50489.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.069720 restraints weight = 38450.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.070253 restraints weight = 32709.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13159  Z= 0.117
  Angle     :  0.541   6.091  17809  Z= 0.293
  Chirality :  0.038   0.203   2002
  Planarity :  0.004   0.071   2217
  Dihedral  :  5.496  52.590   1673
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: -0.24 (0.22), residues: 1504
  helix:  1.26 (0.16), residues: 991
  sheet: -3.18 (0.53), residues: 83
  loop : -2.98 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  14 
 TYR   0.017   0.001   TYR C 177 
 PHE   0.037   0.001   PHE A 255 
 TRP   0.015   0.001   TRP B  79 
 HIS   0.009   0.001   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (13159)
  covalent geometry    : angle       0.54138 (17809)
  hydrogen bonds       : bond        0.04038 (  767)
  hydrogen bonds       : angle       4.43724 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.648 
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: 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: 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: 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: symmetry clash
REVERT: E   96 VAL cc_start: 0.8928 (p) cc_final: 0.8431 (p)
REVERT: D  132 LYS cc_start: 0.9331 (mmtt) cc_final: 0.9001 (mmmm)
REVERT: B  268 LEU cc_start: 0.9341 (mt) cc_final: 0.9138 (mt)
REVERT: B  362 ASP cc_start: 0.8309 (p0) cc_final: 0.8000 (p0)
REVERT: B  400 MET cc_start: 0.9404 (mtp) cc_final: 0.9141 (mtp)
REVERT: A  319 MET cc_start: 0.8240 (ttm) cc_final: 0.7850 (ttm)
REVERT: A  330 ASP cc_start: 0.9182 (t70) cc_final: 0.8877 (t0)
REVERT: A  436 MET cc_start: 0.8756 (mmm) cc_final: 0.8279 (tpp)
REVERT: A  544 HIS cc_start: 0.8384 (m-70) cc_final: 0.7971 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2279
  time to fit residues: 59.4484
Evaluate side-chains
  136 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0970
   chunk 132 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 141 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
C  75 ASN
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.083854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.062985 restraints weight = 166306.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.065582 restraints weight = 79882.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.067171 restraints weight = 51402.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.068120 restraints weight = 39456.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.068661 restraints weight = 33713.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.4525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  13159  Z= 0.180
  Angle     :  0.571   7.464  17809  Z= 0.314
  Chirality :  0.038   0.179   2002
  Planarity :  0.004   0.063   2217
  Dihedral  :  5.421  46.368   1673
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.57 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: -0.31 (0.22), residues: 1504
  helix:  1.20 (0.16), residues: 993
  sheet: -3.14 (0.53), residues: 85
  loop : -3.04 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E  20 
 TYR   0.013   0.001   TYR B 111 
 PHE   0.043   0.002   PHE C 201 
 TRP   0.026   0.001   TRP E  23 
 HIS   0.008   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (13159)
  covalent geometry    : angle       0.57087 (17809)
  hydrogen bonds       : bond        0.04213 (  767)
  hydrogen bonds       : angle       4.65891 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.613 
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: 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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   29 TRP cc_start: 0.8220 (t-100) cc_final: 0.7977 (t-100)
REVERT: E   96 VAL cc_start: 0.8876 (p) cc_final: 0.8438 (p)
REVERT: C  291 ILE cc_start: 0.9350 (mt) cc_final: 0.9121 (mm)
REVERT: D  132 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9054 (mmmm)
REVERT: B  276 LEU cc_start: 0.9214 (mt) cc_final: 0.8809 (mt)
REVERT: A  319 MET cc_start: 0.8185 (ttm) cc_final: 0.7817 (ttm)
REVERT: A  330 ASP cc_start: 0.9212 (t70) cc_final: 0.8945 (t0)
REVERT: A  436 MET cc_start: 0.8820 (mmm) cc_final: 0.8377 (tpp)
REVERT: A  544 HIS cc_start: 0.8414 (m-70) cc_final: 0.7983 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2373
  time to fit residues: 55.8635
Evaluate side-chains
  124 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 137 optimal weight:   10.0000
   chunk 131 optimal weight:    6.9990
   chunk 99 optimal weight:    0.3980
   chunk 138 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 114 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0000
   chunk 117 optimal weight:    3.9990
   overall best weight:    1.2788

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

Flipped N/Q/H residues before XYZ refinement:
C  75 ASN
** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.084571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.063560 restraints weight = 165613.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.066194 restraints weight = 80421.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.067787 restraints weight = 51672.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.068742 restraints weight = 39554.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.069310 restraints weight = 33744.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.4682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  13159  Z= 0.143
  Angle     :  0.549   6.601  17809  Z= 0.301
  Chirality :  0.038   0.185   2002
  Planarity :  0.004   0.055   2217
  Dihedral  :  5.377  46.578   1673
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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: -0.18 (0.22), residues: 1504
  helix:  1.34 (0.16), residues: 988
  sheet: -3.10 (0.52), residues: 85
  loop : -3.04 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  14 
 TYR   0.013   0.001   TYR C 177 
 PHE   0.036   0.001   PHE C 201 
 TRP   0.015   0.001   TRP E  23 
 HIS   0.008   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (13159)
  covalent geometry    : angle       0.54909 (17809)
  hydrogen bonds       : bond        0.04091 (  767)
  hydrogen bonds       : angle       4.52785 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.681 
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: 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: 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: 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: symmetry clash
REVERT: E   96 VAL cc_start: 0.8894 (p) cc_final: 0.8494 (p)
REVERT: C  291 ILE cc_start: 0.9379 (mt) cc_final: 0.9160 (mm)
REVERT: D  132 LYS cc_start: 0.9373 (mmtt) cc_final: 0.9038 (mmmm)
REVERT: B  268 LEU cc_start: 0.9358 (mt) cc_final: 0.9150 (mt)
REVERT: B  276 LEU cc_start: 0.9141 (mt) cc_final: 0.8837 (mt)
REVERT: B  362 ASP cc_start: 0.8280 (p0) cc_final: 0.7980 (p0)
REVERT: A  319 MET cc_start: 0.8201 (ttm) cc_final: 0.7817 (ttm)
REVERT: A  330 ASP cc_start: 0.9187 (t70) cc_final: 0.8922 (t0)
REVERT: A  436 MET cc_start: 0.8806 (mmm) cc_final: 0.8331 (tpp)
REVERT: A  544 HIS cc_start: 0.8396 (m-70) cc_final: 0.7941 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2264
  time to fit residues: 55.1618
Evaluate side-chains
  132 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 129 optimal weight:    5.9990
   chunk 132 optimal weight:   10.0000
   chunk 90 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 113 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 126 optimal weight:    0.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
C  75 ASN
** D  85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.084462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.063577 restraints weight = 163794.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.066182 restraints weight = 78532.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.067747 restraints weight = 50392.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.068699 restraints weight = 38654.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.069270 restraints weight = 32991.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13159  Z= 0.144
  Angle     :  0.538   6.234  17809  Z= 0.295
  Chirality :  0.037   0.181   2002
  Planarity :  0.004   0.054   2217
  Dihedral  :  5.284  45.403   1673
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.97 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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: -0.08 (0.22), residues: 1504
  helix:  1.44 (0.16), residues: 983
  sheet: -3.10 (0.52), residues: 85
  loop : -3.00 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  14 
 TYR   0.013   0.001   TYR C 177 
 PHE   0.032   0.001   PHE C 201 
 TRP   0.013   0.001   TRP B  79 
 HIS   0.008   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (13159)
  covalent geometry    : angle       0.53814 (17809)
  hydrogen bonds       : bond        0.04004 (  767)
  hydrogen bonds       : angle       4.48962 ( 2265)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.715 
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: 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: 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: 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: E   96 VAL cc_start: 0.8882 (p) cc_final: 0.8525 (p)
REVERT: C  291 ILE cc_start: 0.9386 (mt) cc_final: 0.9176 (mm)
REVERT: D  118 MET cc_start: 0.8437 (tpt) cc_final: 0.7992 (tpp)
REVERT: D  132 LYS cc_start: 0.9398 (mmtt) cc_final: 0.9044 (mmmm)
REVERT: D  145 MET cc_start: 0.8604 (tmm) cc_final: 0.8353 (tmm)
REVERT: B  276 LEU cc_start: 0.9239 (mt) cc_final: 0.8862 (mt)
REVERT: B  362 ASP cc_start: 0.8324 (p0) cc_final: 0.8025 (p0)
REVERT: B  400 MET cc_start: 0.9506 (mtp) cc_final: 0.9244 (mtp)
REVERT: A  319 MET cc_start: 0.8196 (ttm) cc_final: 0.7812 (ttm)
REVERT: A  330 ASP cc_start: 0.9201 (t70) cc_final: 0.8941 (t0)
REVERT: A  436 MET cc_start: 0.8795 (mmm) cc_final: 0.8337 (tpp)
REVERT: A  544 HIS cc_start: 0.8349 (m-70) cc_final: 0.7889 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2368
  time to fit residues: 54.4347
Evaluate side-chains
  128 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0870
   chunk 35 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
C  75 ASN
** B 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.085440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.064211 restraints weight = 164214.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.066976 restraints weight = 77669.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.068626 restraints weight = 49148.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.069624 restraints weight = 37356.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.070137 restraints weight = 31719.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  13159  Z= 0.114
  Angle     :  0.515   5.822  17809  Z= 0.280
  Chirality :  0.037   0.186   2002
  Planarity :  0.004   0.055   2217
  Dihedral  :  5.142  45.171   1673
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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:  0.17 (0.23), residues: 1504
  helix:  1.61 (0.17), residues: 990
  sheet: -3.13 (0.51), residues: 85
  loop : -2.90 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  76 
 TYR   0.013   0.001   TYR C 177 
 PHE   0.028   0.001   PHE C 201 
 TRP   0.014   0.001   TRP B  79 
 HIS   0.008   0.001   HIS C 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (13159)
  covalent geometry    : angle       0.51482 (17809)
  hydrogen bonds       : bond        0.03783 (  767)
  hydrogen bonds       : angle       4.29809 ( 2265)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4336.42 seconds
wall clock time: 74 minutes 31.11 seconds (4471.11 seconds total)