Starting phenix.real_space_refine
on Sun Oct 12 04:45:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6me0_9105/10_2025/6me0_9105.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6me0_9105/10_2025/6me0_9105.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6me0_9105/10_2025/6me0_9105.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6me0_9105/10_2025/6me0_9105.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6me0_9105/10_2025/6me0_9105.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6me0_9105/10_2025/6me0_9105.map"
  }
  resolution = 3.6
  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=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     P     845      5.49       5
     Mg     32      5.21       5
     S       8      5.16       5
     Na      1      4.78       5
     C   10256      2.51       5
     N    3976      2.21       5
     O    6421      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 21539
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 17776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 829, 17776
          Classifications: {'RNA': 829}
          Modifications used: {'rna2p_pur': 55, 'rna2p_pyr': 33, 'rna3p_pur': 414, 'rna3p_pyr': 327}
          Link IDs: {'rna2p': 88, 'rna3p': 740}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 337
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "C"
      Number of atoms: 3393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3393
          Classifications: {'peptide': 414}
          Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 398}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 33
          Unusual residues: {' MG': 32, ' NA': 1}
          Classifications: {'undetermined': 33}
          Link IDs: {None: 32}
  Time building chain proxies: 4.72, per 1000 atoms: 0.22
  Number of scatterers: 21539
  At special positions: 0
  Unit cell: (111.39, 160.37, 233.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S       8     16.00
     P     845     15.00
     Mg     32     11.99
     Na      1     11.00
     O    6421      8.00
     N    3976      7.00
     C   10256      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.94
  Conformation dependent library (CDL) restraints added in 332.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  776

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 4 sheets defined
      54.1% alpha, 7.2% beta
      291 base pairs and 472 stacking pairs defined.
    Time for finding SS restraints: 3.99
  Creating SS restraints...
    Processing helix  chain 'C' and resid 27 through 47
      removed outlier: 3.791A  pdb=" N   ASN C  32 " --> pdb=" O   TRP C  28 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   ARG C  33 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL C  35 " --> pdb=" O   ALA C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 63
    Processing helix  chain 'C' and resid 64 through 77
    Processing helix  chain 'C' and resid 93 through 105
      removed outlier: 3.702A  pdb=" N   LEU C 104 " --> pdb=" O   ALA C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 133 through 154
      Proline residue:  C 149  - end of helix
      removed outlier: 3.768A  pdb=" N   THR C 153 " --> pdb=" O   PRO C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 179
    Processing helix  chain 'C' and resid 201 through 208
    Processing helix  chain 'C' and resid 212 through 222
      removed outlier: 3.534A  pdb=" N   SER C 222 " --> pdb=" O   LYS C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 251
    Processing helix  chain 'C' and resid 254 through 259
    Processing helix  chain 'C' and resid 285 through 301
      removed outlier: 3.750A  pdb=" N   GLU C 300 " --> pdb=" O   GLU C 296 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ARG C 301 " --> pdb=" O   PHE C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 356
      removed outlier: 3.661A  pdb=" N   LYS C 343 " --> pdb=" O   LYS C 339 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA C 344 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE C 345 " --> pdb=" O   ASN C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 360 through 379
      Proline residue:  C 370  - end of helix
      removed outlier: 3.880A  pdb=" N   HIS C 379 " --> pdb=" O   TRP C 375 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 407
      removed outlier: 3.898A  pdb=" N   HIS C 407 " --> pdb=" O   ALA C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 411 through 419
      removed outlier: 3.805A  pdb=" N   THR C 415 " --> pdb=" O   PRO C 411 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 452
    Processing sheet with id=AA1, first strand: chain 'C' and resid 115 through 119
      removed outlier: 3.621A  pdb=" N   VAL C 117 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE C 119 " --> pdb=" O   ARG C 127 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 270 through 273
    Processing sheet with id=AA3, first strand: chain 'C' and resid 319 through 321
    Processing sheet with id=AA4, first strand: chain 'C' and resid 420 through 421

    165 hydrogen bonds defined for protein.
    462 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      755 hydrogen bonds
      1294 hydrogen bond angles
      0 basepair planarities
      291 basepair parallelities
      472 stacking parallelities
  Total time for adding SS restraints: 7.61

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2097
        1.32 -     1.44: 11238
        1.44 -     1.56: 8713
        1.56 -     1.67: 1688
        1.67 -     1.79: 12
  Bond restraints: 23748
  Sorted by residual:
  bond pdb=" O3'   U A   1 "
       pdb=" P     U A   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.460  0.147 1.50e-02 4.44e+03 9.66e+01
  bond pdb=" CA  HIS C 379 "
       pdb=" CB  HIS C 379 "
    ideal  model  delta    sigma   weight residual
    1.526  1.444  0.082 1.76e-02 3.23e+03 2.19e+01
  bond pdb=" N   PRO C 149 "
       pdb=" CD  PRO C 149 "
    ideal  model  delta    sigma   weight residual
    1.473  1.430  0.043 1.40e-02 5.10e+03 9.38e+00
  bond pdb=" N   PRO C 113 "
       pdb=" CD  PRO C 113 "
    ideal  model  delta    sigma   weight residual
    1.473  1.430  0.043 1.40e-02 5.10e+03 9.35e+00
  bond pdb=" N   PRO C 132 "
       pdb=" CD  PRO C 132 "
    ideal  model  delta    sigma   weight residual
    1.473  1.432  0.041 1.40e-02 5.10e+03 8.70e+00
  ... (remaining 23743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 34957
        2.61 -     5.22: 1169
        5.22 -     7.83: 142
        7.83 -    10.44: 18
       10.44 -    13.04: 6
  Bond angle restraints: 36292
  Sorted by residual:
  angle pdb=" N   ILE C  89 "
        pdb=" CA  ILE C  89 "
        pdb=" C   ILE C  89 "
      ideal   model   delta    sigma   weight residual
     112.12  106.27    5.85 8.40e-01 1.42e+00 4.84e+01
  angle pdb=" C   GLN C 228 "
        pdb=" N   GLN C 229 "
        pdb=" CA  GLN C 229 "
      ideal   model   delta    sigma   weight residual
     121.94  132.47  -10.53 1.76e+00 3.23e-01 3.58e+01
  angle pdb=" N   GLU C 317 "
        pdb=" CA  GLU C 317 "
        pdb=" C   GLU C 317 "
      ideal   model   delta    sigma   weight residual
     114.39  106.14    8.25 1.45e+00 4.76e-01 3.24e+01
  angle pdb=" C3'   U A 477 "
        pdb=" O3'   U A 477 "
        pdb=" P     G A 478 "
      ideal   model   delta    sigma   weight residual
     120.20  128.07   -7.87 1.50e+00 4.44e-01 2.75e+01
  angle pdb=" C   LYS C 416 "
        pdb=" N   ASN C 417 "
        pdb=" CA  ASN C 417 "
      ideal   model   delta    sigma   weight residual
     122.54  114.15    8.39 1.65e+00 3.67e-01 2.59e+01
  ... (remaining 36287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.90: 12912
       35.90 -    71.81: 2006
       71.81 -   107.71: 257
      107.71 -   143.61: 8
      143.61 -   179.52: 8
  Dihedral angle restraints: 15191
    sinusoidal: 13993
      harmonic: 1198
  Sorted by residual:
  dihedral pdb=" CA  TYR C 273 "
           pdb=" C   TYR C 273 "
           pdb=" N   ALA C 274 "
           pdb=" CA  ALA C 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.23  -44.77     0      5.00e+00 4.00e-02 8.02e+01
  dihedral pdb=" O4'   U A 839 "
           pdb=" C1'   U A 839 "
           pdb=" N1    U A 839 "
           pdb=" C2    U A 839 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   52.75  147.25     1      1.50e+01 4.44e-03 7.86e+01
  dihedral pdb=" O4'   U A 258 "
           pdb=" C1'   U A 258 "
           pdb=" N1    U A 258 "
           pdb=" C2    U A 258 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.48  179.52     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 15188 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 3998
       0.074 -    0.147: 626
       0.147 -    0.221: 69
       0.221 -    0.294: 10
       0.294 -    0.368: 5
  Chirality restraints: 4708
  Sorted by residual:
  chirality pdb=" C3'   G A 832 "
            pdb=" C4'   G A 832 "
            pdb=" O3'   G A 832 "
            pdb=" C2'   G A 832 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.11   -0.37 2.00e-01 2.50e+01 3.38e+00
  chirality pdb=" C3'   U A 764 "
            pdb=" C4'   U A 764 "
            pdb=" O3'   U A 764 "
            pdb=" C2'   U A 764 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.12   -0.36 2.00e-01 2.50e+01 3.20e+00
  chirality pdb=" C3'   U A 545 "
            pdb=" C4'   U A 545 "
            pdb=" O3'   U A 545 "
            pdb=" C2'   U A 545 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.39   -0.35 2.00e-01 2.50e+01 3.11e+00
  ... (remaining 4705 not shown)

  Planarity restraints: 1430
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A  56 "   -0.011 2.00e-02 2.50e+03   2.73e-02 2.24e+01
        pdb=" N9    G A  56 "    0.004 2.00e-02 2.50e+03
        pdb=" C8    G A  56 "    0.007 2.00e-02 2.50e+03
        pdb=" N7    G A  56 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    G A  56 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G A  56 "    0.023 2.00e-02 2.50e+03
        pdb=" O6    G A  56 "   -0.021 2.00e-02 2.50e+03
        pdb=" N1    G A  56 "   -0.009 2.00e-02 2.50e+03
        pdb=" C2    G A  56 "    0.075 2.00e-02 2.50e+03
        pdb=" N2    G A  56 "   -0.045 2.00e-02 2.50e+03
        pdb=" N3    G A  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    G A  56 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 113 "   -0.044 2.00e-02 2.50e+03   1.93e-02 1.12e+01
        pdb=" N9    G A 113 "    0.042 2.00e-02 2.50e+03
        pdb=" C8    G A 113 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G A 113 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    G A 113 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G A 113 "   -0.020 2.00e-02 2.50e+03
        pdb=" O6    G A 113 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G A 113 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G A 113 "    0.004 2.00e-02 2.50e+03
        pdb=" N2    G A 113 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G A 113 "    0.016 2.00e-02 2.50e+03
        pdb=" C4    G A 113 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 262 "    0.043 2.00e-02 2.50e+03   1.84e-02 9.28e+00
        pdb=" N9    A A 262 "   -0.031 2.00e-02 2.50e+03
        pdb=" C8    A A 262 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7    A A 262 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    A A 262 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    A A 262 "    0.000 2.00e-02 2.50e+03
        pdb=" N6    A A 262 "    0.024 2.00e-02 2.50e+03
        pdb=" N1    A A 262 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    A A 262 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    A A 262 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A A 262 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1427 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.20: 30
        2.20 -     2.88: 7348
        2.88 -     3.55: 34573
        3.55 -     4.23: 69641
        4.23 -     4.90: 86898
  Nonbonded interactions: 198490
  Sorted by model distance:
  nonbonded pdb=" P     U A   1 "
            pdb=" O2'   A A 860 "
     model   vdw
     1.531 3.400
  nonbonded pdb=" O   LEU C 356 "
            pdb=" CH2 TRP C 402 "
     model   vdw
     1.616 3.340
  nonbonded pdb=" CZ2 TRP C  28 "
            pdb=" CD  LYS C  73 "
     model   vdw
     1.671 3.740
  nonbonded pdb=" OD1 ASP C 366 "
            pdb=" NH2 ARG C 444 "
     model   vdw
     1.693 3.120
  nonbonded pdb=" O2    U A   1 "
            pdb=" N1    G A 865 "
     model   vdw
     1.696 3.120
  ... (remaining 198485 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     26.000
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
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      :  0.010   0.344  23749  Z= 0.550
  Angle     :  1.156  13.045  36292  Z= 0.564
  Chirality :  0.055   0.368   4708
  Planarity :  0.007   0.070   1430
  Dihedral  : 25.122 179.517  14415
  Min Nonbonded Distance : 1.531

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 1.26 %

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 aren not related in a simple way.
  whole: -5.11 (0.30), residues: 408
  helix: -2.85 (0.24), residues: 212
  sheet: -2.47 (0.72), residues: 36
  loop : -4.27 (0.38), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.002   ARG C 163 
 TYR   0.035   0.004   TYR C 378 
 PHE   0.039   0.005   PHE C 231 
 TRP   0.042   0.005   TRP C 204 
 HIS   0.016   0.004   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00965 (23748)
  covalent geometry    : angle       1.15553 (36292)
  hydrogen bonds       : bond        0.13169 (  920)
  hydrogen bonds       : angle       4.23243 ( 1756)
  Misc. bond           : bond        0.34354 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   47 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7721 (ptpt)
REVERT: C   65 PHE cc_start: 0.8403 (t80) cc_final: 0.8201 (t80)
REVERT: C  118 TYR cc_start: 0.8201 (m-80) cc_final: 0.7976 (m-80)
REVERT: C  276 ASP cc_start: 0.7764 (m-30) cc_final: 0.7361 (m-30)
REVERT: C  429 VAL cc_start: 0.9186 (t) cc_final: 0.8923 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.2732
  time to fit residues: 34.5289
Evaluate side-chains
  54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 123 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
C  32 ASN
C 202 HIS
** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 269 ASN
C 314 HIS
C 346 HIS
C 369 ASN
C 377 ASN
C 407 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.098642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.076115 restraints weight = 73125.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.078078 restraints weight = 29036.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.079166 restraints weight = 17384.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.079518 restraints weight = 13322.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.079731 restraints weight = 12382.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  23749  Z= 0.203
  Angle     :  0.682   8.950  36292  Z= 0.346
  Chirality :  0.035   0.253   4708
  Planarity :  0.005   0.079   1430
  Dihedral  : 25.450 178.689  13552
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.56 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  7.04 %
    Favored  : 90.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 aren not related in a simple way.
  whole: -3.58 (0.36), residues: 408
  helix: -1.03 (0.32), residues: 216
  sheet: -2.28 (0.77), residues: 36
  loop : -4.41 (0.38), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 116 
 TYR   0.014   0.002   TYR C 187 
 PHE   0.031   0.003   PHE C 231 
 TRP   0.037   0.003   TRP C 396 
 HIS   0.008   0.002   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (23748)
  covalent geometry    : angle       0.68162 (36292)
  hydrogen bonds       : bond        0.07368 (  920)
  hydrogen bonds       : angle       3.07130 ( 1756)
  Misc. bond           : bond        0.00270 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.356 
Fit side-chains
REVERT: C   51 TRP cc_start: 0.8954 (m100) cc_final: 0.8479 (m-10)
REVERT: C   65 PHE cc_start: 0.8143 (t80) cc_final: 0.7825 (t80)
REVERT: C   66 TYR cc_start: 0.7532 (m-80) cc_final: 0.6340 (m-80)
REVERT: C  110 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8575 (tppt)
REVERT: C  118 TYR cc_start: 0.8226 (m-80) cc_final: 0.7599 (m-80)
REVERT: C  246 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7454 (mpp)
REVERT: C  317 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6742 (tm-30)
  outliers start: 9
  outliers final: 5
  residues processed: 64
  average time/residue: 0.2435
  time to fit residues: 21.6847
Evaluate side-chains
  52 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  284 LYS
Chi-restraints excluded: chain C residue  314 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 80 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 57 optimal weight:    6.9990
   chunk 42 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
C  58 GLN
** C  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 314 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.095404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.072582 restraints weight = 74483.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.074425 restraints weight = 30445.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.075279 restraints weight = 18795.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.075912 restraints weight = 14850.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.075980 restraints weight = 13491.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  23749  Z= 0.385
  Angle     :  0.847   9.269  36292  Z= 0.423
  Chirality :  0.042   0.287   4708
  Planarity :  0.006   0.043   1430
  Dihedral  : 25.597 177.515  13552
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 19.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.75 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  :  8.73 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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 aren not related in a simple way.
  whole: -3.40 (0.37), residues: 408
  helix: -0.87 (0.32), residues: 220
  sheet: -2.36 (0.79), residues: 36
  loop : -4.40 (0.38), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C 116 
 TYR   0.032   0.003   TYR C 378 
 PHE   0.027   0.003   PHE C 231 
 TRP   0.044   0.004   TRP C 226 
 HIS   0.021   0.004   HIS C 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00739 (23748)
  covalent geometry    : angle       0.84736 (36292)
  hydrogen bonds       : bond        0.08922 (  920)
  hydrogen bonds       : angle       3.33162 ( 1756)
  Misc. bond           : bond        0.01332 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: C   65 PHE cc_start: 0.8237 (t80) cc_final: 0.7926 (t80)
REVERT: C   66 TYR cc_start: 0.7615 (m-80) cc_final: 0.6450 (m-80)
REVERT: C  110 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8602 (tppt)
REVERT: C  246 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7352 (mpp)
REVERT: C  250 MET cc_start: 0.8775 (mmm) cc_final: 0.8569 (mmm)
REVERT: C  397 HIS cc_start: 0.7935 (t-90) cc_final: 0.7733 (t-90)
  outliers start: 15
  outliers final: 7
  residues processed: 59
  average time/residue: 0.1895
  time to fit residues: 16.6005
Evaluate side-chains
  47 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  422 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   chunk 113 optimal weight:    0.6980
   chunk 7 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9990
   chunk 115 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 74 optimal weight:    8.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
C  58 GLN
C  63 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.097696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.074962 restraints weight = 73956.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.076833 restraints weight = 29555.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.078025 restraints weight = 17973.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.078324 restraints weight = 13594.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.078517 restraints weight = 12841.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  23749  Z= 0.228
  Angle     :  0.688   9.381  36292  Z= 0.348
  Chirality :  0.035   0.249   4708
  Planarity :  0.005   0.077   1430
  Dihedral  : 25.424 179.149  13552
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.82 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 12.11 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 aren not related in a simple way.
  whole: -3.00 (0.38), residues: 408
  helix: -0.50 (0.33), residues: 222
  sheet: -2.24 (0.79), residues: 36
  loop : -4.31 (0.39), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 426 
 TYR   0.016   0.003   TYR C 378 
 PHE   0.021   0.002   PHE C 231 
 TRP   0.050   0.003   TRP C 226 
 HIS   0.004   0.002   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (23748)
  covalent geometry    : angle       0.68761 (36292)
  hydrogen bonds       : bond        0.07467 (  920)
  hydrogen bonds       : angle       2.98600 ( 1756)
  Misc. bond           : bond        0.01115 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: C   65 PHE cc_start: 0.8132 (t80) cc_final: 0.7759 (t80)
REVERT: C  110 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8606 (tppt)
REVERT: C  246 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7425 (mpp)
REVERT: C  300 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7436 (mp0)
REVERT: C  317 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7389 (tm-30)
REVERT: C  397 HIS cc_start: 0.7939 (t-90) cc_final: 0.7645 (t-90)
  outliers start: 12
  outliers final: 6
  residues processed: 54
  average time/residue: 0.2006
  time to fit residues: 16.0107
Evaluate side-chains
  51 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  349 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 61 optimal weight:   20.0000
   chunk 1 optimal weight:    6.9990
   chunk 81 optimal weight:   10.0000
   chunk 91 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 41 optimal weight:    8.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
C  58 GLN
C 262 HIS
** C 389 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 = 0.3728 r_free = 0.3728 target = 0.095060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.072236 restraints weight = 74058.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.074099 restraints weight = 30545.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.074943 restraints weight = 18753.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.075496 restraints weight = 14957.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.075665 restraints weight = 13699.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.065  23749  Z= 0.397
  Angle     :  0.851   9.598  36292  Z= 0.423
  Chirality :  0.042   0.269   4708
  Planarity :  0.006   0.062   1430
  Dihedral  : 25.600 178.219  13552
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 19.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.46 %
    Favored  : 85.54 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 12.11 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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 aren not related in a simple way.
  whole: -3.05 (0.38), residues: 408
  helix: -0.65 (0.33), residues: 217
  sheet: -1.99 (0.86), residues: 36
  loop : -4.10 (0.41), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 426 
 TYR   0.023   0.003   TYR C 378 
 PHE   0.022   0.003   PHE C 231 
 TRP   0.076   0.004   TRP C 226 
 HIS   0.008   0.003   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00759 (23748)
  covalent geometry    : angle       0.85140 (36292)
  hydrogen bonds       : bond        0.08989 (  920)
  hydrogen bonds       : angle       3.35535 ( 1756)
  Misc. bond           : bond        0.01038 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 43
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   66 TYR cc_start: 0.7605 (m-80) cc_final: 0.6866 (m-80)
REVERT: C  105 ARG cc_start: 0.5943 (ttp-170) cc_final: 0.5692 (ttp-110)
REVERT: C  246 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7478 (mpp)
REVERT: C  300 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7500 (mp0)
  outliers start: 20
  outliers final: 12
  residues processed: 57
  average time/residue: 0.1991
  time to fit residues: 16.6673
Evaluate side-chains
  58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  226 TRP
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  429 VAL
Chi-restraints excluded: chain C residue  445 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 88 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 66 optimal weight:   20.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  58 GLN
C 262 HIS
** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 389 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 = 0.3720 r_free = 0.3720 target = 0.094629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.071736 restraints weight = 74631.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.073615 restraints weight = 30691.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.074421 restraints weight = 18832.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.075071 restraints weight = 15056.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.075164 restraints weight = 13685.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.070  23749  Z= 0.444
  Angle     :  0.889  10.197  36292  Z= 0.439
  Chirality :  0.044   0.274   4708
  Planarity :  0.006   0.058   1430
  Dihedral  : 25.612 179.314  13552
  Min Nonbonded Distance : 1.796

Molprobity Statistics.
  All-atom Clashscore : 21.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.24 %
    Favored  : 86.76 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 14.65 %
    Favored  : 79.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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 aren not related in a simple way.
  whole: -3.30 (0.38), residues: 408
  helix: -0.82 (0.33), residues: 215
  sheet: -2.25 (0.85), residues: 36
  loop : -4.20 (0.41), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 157 
 TYR   0.026   0.004   TYR C 378 
 PHE   0.031   0.004   PHE C  65 
 TRP   0.074   0.004   TRP C 226 
 HIS   0.009   0.003   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00850 (23748)
  covalent geometry    : angle       0.88859 (36292)
  hydrogen bonds       : bond        0.09265 (  920)
  hydrogen bonds       : angle       3.42765 ( 1756)
  Misc. bond           : bond        0.00710 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   66 TYR cc_start: 0.7736 (m-80) cc_final: 0.6996 (m-80)
REVERT: C  246 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7491 (mpp)
REVERT: C  300 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7535 (mp0)
  outliers start: 21
  outliers final: 15
  residues processed: 59
  average time/residue: 0.2092
  time to fit residues: 17.9724
Evaluate side-chains
  59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  226 TRP
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain C residue  422 LYS
Chi-restraints excluded: chain C residue  429 VAL
Chi-restraints excluded: chain C residue  445 TYR
Chi-restraints excluded: chain C residue  456 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  58 GLN
C 262 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.096373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.073567 restraints weight = 73958.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.075481 restraints weight = 30184.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.076340 restraints weight = 18353.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.076866 restraints weight = 14626.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.077079 restraints weight = 13322.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  23749  Z= 0.288
  Angle     :  0.741  10.138  36292  Z= 0.373
  Chirality :  0.038   0.254   4708
  Planarity :  0.006   0.049   1430
  Dihedral  : 25.525 178.933  13552
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 17.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.73 %
    Favored  : 86.27 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 16.62 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 aren not related in a simple way.
  whole: -3.10 (0.39), residues: 408
  helix: -0.69 (0.33), residues: 217
  sheet: -2.26 (0.84), residues: 36
  loop : -4.06 (0.41), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 116 
 TYR   0.020   0.003   TYR C  66 
 PHE   0.023   0.003   PHE C  65 
 TRP   0.065   0.003   TRP C 226 
 HIS   0.005   0.002   HIS C 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 (23748)
  covalent geometry    : angle       0.74107 (36292)
  hydrogen bonds       : bond        0.08021 (  920)
  hydrogen bonds       : angle       3.13479 ( 1756)
  Misc. bond           : bond        0.00782 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   66 TYR cc_start: 0.7804 (m-80) cc_final: 0.6729 (m-80)
REVERT: C  246 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7498 (mpp)
REVERT: C  300 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7484 (mp0)
REVERT: C  397 HIS cc_start: 0.7886 (t-90) cc_final: 0.7629 (t-90)
  outliers start: 16
  outliers final: 11
  residues processed: 58
  average time/residue: 0.2004
  time to fit residues: 17.1720
Evaluate side-chains
  55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  226 TRP
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  284 LYS
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 61 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 53 optimal weight:    9.9990
   chunk 59 optimal weight:    8.9990
   chunk 117 optimal weight:    0.9980
   chunk 73 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   overall best weight:    5.9988

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

Flipped N/Q/H residues before XYZ refinement:
C  58 GLN
** C 341 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 = 0.3700 r_free = 0.3700 target = 0.093636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.070851 restraints weight = 74598.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.072678 restraints weight = 31160.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.073473 restraints weight = 19458.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.074115 restraints weight = 15490.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.074256 restraints weight = 14059.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.081  23749  Z= 0.509
  Angle     :  0.974  10.918  36292  Z= 0.480
  Chirality :  0.048   0.295   4708
  Planarity :  0.007   0.070   1430
  Dihedral  : 25.737 178.008  13552
  Min Nonbonded Distance : 1.790

Molprobity Statistics.
  All-atom Clashscore : 23.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.95 %
    Favored  : 85.05 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 17.46 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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 aren not related in a simple way.
  whole: -3.61 (0.37), residues: 408
  helix: -1.13 (0.33), residues: 216
  sheet: -1.94 (0.89), residues: 34
  loop : -4.38 (0.38), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 105 
 TYR   0.024   0.004   TYR C 378 
 PHE   0.032   0.004   PHE C  65 
 TRP   0.065   0.004   TRP C 226 
 HIS   0.009   0.003   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00974 (23748)
  covalent geometry    : angle       0.97439 (36292)
  hydrogen bonds       : bond        0.10094 (  920)
  hydrogen bonds       : angle       3.56310 ( 1756)
  Misc. bond           : bond        0.00779 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  246 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7529 (mpp)
REVERT: C  300 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7541 (mp0)
  outliers start: 21
  outliers final: 15
  residues processed: 60
  average time/residue: 0.2008
  time to fit residues: 17.6438
Evaluate side-chains
  60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  226 TRP
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  253 ASP
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  284 LYS
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  422 LYS
Chi-restraints excluded: chain C residue  429 VAL
Chi-restraints excluded: chain C residue  445 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 120 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
C  58 GLN
C 208 ASN
C 262 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.096315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.073538 restraints weight = 74024.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.075420 restraints weight = 30358.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.076389 restraints weight = 18410.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.076806 restraints weight = 14538.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.077010 restraints weight = 13500.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  23749  Z= 0.289
  Angle     :  0.745   9.148  36292  Z= 0.375
  Chirality :  0.038   0.253   4708
  Planarity :  0.005   0.054   1430
  Dihedral  : 25.551 179.237  13552
  Min Nonbonded Distance : 1.834

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.01 %
    Favored  : 87.99 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 19.44 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 aren not related in a simple way.
  whole: -3.25 (0.38), residues: 408
  helix: -0.80 (0.34), residues: 217
  sheet: -1.95 (0.88), residues: 34
  loop : -4.24 (0.39), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 105 
 TYR   0.017   0.002   TYR C 109 
 PHE   0.016   0.002   PHE C 231 
 TRP   0.060   0.003   TRP C 226 
 HIS   0.005   0.002   HIS C 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 (23748)
  covalent geometry    : angle       0.74533 (36292)
  hydrogen bonds       : bond        0.08084 (  920)
  hydrogen bonds       : angle       3.14856 ( 1756)
  Misc. bond           : bond        0.00737 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 44
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  246 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7520 (mpp)
REVERT: C  300 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7986 (mp0)
REVERT: C  397 HIS cc_start: 0.7912 (t-90) cc_final: 0.7581 (t-90)
  outliers start: 18
  outliers final: 14
  residues processed: 58
  average time/residue: 0.1825
  time to fit residues: 15.8737
Evaluate side-chains
  60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  208 ASN
Chi-restraints excluded: chain C residue  226 TRP
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  253 ASP
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  284 LYS
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  421 ILE
Chi-restraints excluded: chain C residue  429 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   chunk 70 optimal weight:    8.9990
   chunk 123 optimal weight:    2.9990
   chunk 9 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 118 optimal weight:    0.8980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
C  58 GLN
C 208 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.098708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.076064 restraints weight = 73763.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.077954 restraints weight = 29536.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.079090 restraints weight = 17942.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.079380 restraints weight = 13808.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.079624 restraints weight = 12944.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  23749  Z= 0.197
  Angle     :  0.649  10.495  36292  Z= 0.327
  Chirality :  0.033   0.246   4708
  Planarity :  0.005   0.059   1430
  Dihedral  : 25.289 179.244  13552
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 14.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 19.72 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 aren not related in a simple way.
  whole: -2.66 (0.40), residues: 408
  helix: -0.24 (0.34), residues: 217
  sheet: -2.11 (0.85), residues: 36
  loop : -4.00 (0.41), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 105 
 TYR   0.012   0.002   TYR C 109 
 PHE   0.014   0.002   PHE C 231 
 TRP   0.056   0.003   TRP C 226 
 HIS   0.003   0.001   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (23748)
  covalent geometry    : angle       0.64895 (36292)
  hydrogen bonds       : bond        0.07137 (  920)
  hydrogen bonds       : angle       2.92383 ( 1756)
  Misc. bond           : bond        0.00690 (    1)

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

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

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  816 Ramachandran restraints generated.
    408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   66 TYR cc_start: 0.7698 (m-80) cc_final: 0.6747 (m-80)
REVERT: C  203 GLU cc_start: 0.7681 (pm20) cc_final: 0.7356 (pm20)
REVERT: C  246 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7609 (mpp)
REVERT: C  300 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7475 (mp0)
REVERT: C  317 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7548 (tp30)
REVERT: C  392 ASP cc_start: 0.7684 (m-30) cc_final: 0.7269 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 57
  average time/residue: 0.1804
  time to fit residues: 15.4165
Evaluate side-chains
  57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  116 ARG
Chi-restraints excluded: chain C residue  167 CYS
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  226 TRP
Chi-restraints excluded: chain C residue  246 MET
Chi-restraints excluded: chain C residue  253 ASP
Chi-restraints excluded: chain C residue  282 GLU
Chi-restraints excluded: chain C residue  300 GLU
Chi-restraints excluded: chain C residue  314 HIS
Chi-restraints excluded: chain C residue  349 ILE
Chi-restraints excluded: chain C residue  421 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  58 GLN
C 208 ASN
C 262 HIS
** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.094869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.072036 restraints weight = 74531.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.073875 restraints weight = 30825.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.074809 restraints weight = 18898.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.075263 restraints weight = 14984.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.075460 restraints weight = 13864.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.067  23749  Z= 0.443
  Angle     :  0.873  10.210  36292  Z= 0.432
  Chirality :  0.043   0.261   4708
  Planarity :  0.006   0.066   1430
  Dihedral  : 25.547 178.621  13552
  Min Nonbonded Distance : 1.809

Molprobity Statistics.
  All-atom Clashscore : 20.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.95 %
    Favored  : 85.05 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 20.00 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.25 %
    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 aren not related in a simple way.
  whole: -3.26 (0.38), residues: 408
  helix: -0.81 (0.33), residues: 217
  sheet: -1.89 (0.87), residues: 34
  loop : -4.26 (0.39), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 157 
 TYR   0.021   0.003   TYR C 109 
 PHE   0.019   0.003   PHE C 231 
 TRP   0.059   0.003   TRP C 226 
 HIS   0.007   0.003   HIS C 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00846 (23748)
  covalent geometry    : angle       0.87265 (36292)
  hydrogen bonds       : bond        0.09158 (  920)
  hydrogen bonds       : angle       3.32425 ( 1756)
  Misc. bond           : bond        0.00738 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3598.07 seconds
wall clock time: 63 minutes 20.17 seconds (3800.17 seconds total)