Starting phenix.real_space_refine
on Wed Aug  5 22:45:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11ic_75710/08_2026/11ic_75710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11ic_75710/08_2026/11ic_75710.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11ic_75710/08_2026/11ic_75710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11ic_75710/08_2026/11ic_75710.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11ic_75710/08_2026/11ic_75710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11ic_75710/08_2026/11ic_75710.map"
  }
  resolution = 2.63
  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=   0.013
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     203      5.49       5
     Mg      1      5.21       5
     S      17      5.16       5
     C    3610      2.51       5
     N    1295      2.21       5
     O    1875      1.98       5
     H    4938      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11939
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 5411
          Classifications: {'peptide': 334}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 316}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 6035
          Classifications: {'RNA': 187}
          Modifications used: {'3*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 13, 'rna3p_pur': 93, 'rna3p_pyr': 64}
          Link IDs: {'rna2p': 29, 'rna3p': 157}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 492
          Classifications: {'RNA': 16}
          Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 14}
          Link IDs: {'rna3p': 15}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.81, per 1000 atoms: 0.15
  Number of scatterers: 11939
  At special positions: 0
  Unit cell: (88.275, 123.75, 123.75, 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      17     16.00
     P     203     15.00
     Mg      1     11.99
     O    1875      8.00
     N    1295      7.00
     C    3610      6.00
     H    4938      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: 0.86
  Conformation dependent library (CDL) restraints added in 244.3 milliseconds
  

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  634

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 4 sheets defined
      37.4% alpha, 14.1% beta
      72 base pairs and 126 stacking pairs defined.
    Time for finding SS restraints: 1.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 29
    Processing helix  chain 'A' and resid 88 through 108
      removed outlier: 4.570A  pdb=" N   LYS A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 121
    Processing helix  chain 'A' and resid 163 through 184
      removed outlier: 3.893A  pdb=" N   ILE A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 314
      Proline residue:  A 304  - end of helix
      removed outlier: 3.530A  pdb=" N   ASP A 312 " --> pdb=" O   ASP A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 333
    Processing helix  chain 'A' and resid 338 through 340
      No H-bonds generated for 'chain 'A' and resid 338 through 340'
    Processing helix  chain 'A' and resid 341 through 349
    Processing helix  chain 'A' and resid 408 through 415
    Processing helix  chain 'A' and resid 417 through 423
      removed outlier: 3.714A  pdb=" N   LYS A 423 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17
      removed outlier: 5.280A  pdb=" N   MET A  15 " --> pdb=" O   VAL A   6 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   VAL A   6 " --> pdb=" O   MET A  15 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   TYR A   5 " --> pdb=" O   ILE A  42 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   LEU A  44 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   ILE A   7 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 191
      removed outlier: 6.493A  pdb=" N   LEU A  55 " --> pdb=" O   LYS A 188 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   VAL A 190 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   ILE A  66 " --> pdb=" O   GLN A  82 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   GLN A  82 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   MET A  68 " --> pdb=" O   ASN A  80 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   ASN A  80 " --> pdb=" O   MET A  68 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   VAL A  70 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLN A  82 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 367 " --> pdb=" O   GLN A  82 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131
    Processing sheet with id=AA4, first strand: chain 'A' and resid 392 through 395
      removed outlier: 6.922A  pdb=" N   TYR A 387 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)

    101 hydrogen bonds defined for protein.
    285 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      183 hydrogen bonds
      338 hydrogen bond angles
      0 basepair planarities
      72 basepair parallelities
      126 stacking parallelities
  Total time for adding SS restraints: 2.73

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 4930
        1.03 -     1.22: 51
        1.22 -     1.42: 3395
        1.42 -     1.61: 4099
        1.61 -     1.81: 29
  Bond restraints: 12504
  Sorted by residual:
  bond pdb=" N9    A B 117 "
       pdb=" C4    A B 117 "
    ideal  model  delta    sigma   weight residual
    1.374  1.362  0.012 6.00e-03 2.78e+04 4.18e+00
  bond pdb=" N9    A B 189 "
       pdb=" C4    A B 189 "
    ideal  model  delta    sigma   weight residual
    1.374  1.363  0.011 6.00e-03 2.78e+04 3.34e+00
  bond pdb=" N3    A B 189 "
       pdb=" C4    A B 189 "
    ideal  model  delta    sigma   weight residual
    1.344  1.333  0.011 6.00e-03 2.78e+04 3.19e+00
  bond pdb=" N3    A B 117 "
       pdb=" C4    A B 117 "
    ideal  model  delta    sigma   weight residual
    1.344  1.334  0.010 6.00e-03 2.78e+04 2.79e+00
  bond pdb=" C1'   A C   9 "
       pdb=" N9    A C   9 "
    ideal  model  delta    sigma   weight residual
    1.483  1.458  0.025 1.50e-02 4.44e+03 2.70e+00
  ... (remaining 12499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 20962
        1.48 -     2.96: 1356
        2.96 -     4.44: 148
        4.44 -     5.91: 11
        5.91 -     7.39: 5
  Bond angle restraints: 22482
  Sorted by residual:
  angle pdb=" O5'   U C   7 "
        pdb=" C5'   U C   7 "
        pdb=" C4'   U C   7 "
      ideal   model   delta    sigma   weight residual
     109.40  113.61   -4.21 8.00e-01 1.56e+00 2.77e+01
  angle pdb=" C1'   U B  97 "
        pdb=" N1    U B  97 "
        pdb=" C2    U B  97 "
      ideal   model   delta    sigma   weight residual
     117.70  123.88   -6.18 1.20e+00 6.94e-01 2.65e+01
  angle pdb=" O5'   A B  48 "
        pdb=" C5'   A B  48 "
        pdb=" C4'   A B  48 "
      ideal   model   delta    sigma   weight residual
     109.40  112.96   -3.56 8.00e-01 1.56e+00 1.98e+01
  angle pdb=" C4'   A C   9 "
        pdb=" C3'   A C   9 "
        pdb=" C2'   A C   9 "
      ideal   model   delta    sigma   weight residual
     102.60   98.23    4.37 1.00e+00 1.00e+00 1.91e+01
  angle pdb=" N1    U B  97 "
        pdb=" C2    U B  97 "
        pdb=" O2    U B  97 "
      ideal   model   delta    sigma   weight residual
     122.80  125.85   -3.05 7.00e-01 2.04e+00 1.90e+01
  ... (remaining 22477 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.31: 5455
       33.31 -    66.62: 570
       66.62 -    99.93: 73
       99.93 -   133.24: 3
      133.24 -   166.55: 8
  Dihedral angle restraints: 6109
    sinusoidal: 4993
      harmonic: 1116
  Sorted by residual:
  dihedral pdb=" O4'   C B  49 "
           pdb=" C1'   C B  49 "
           pdb=" N1    C B  49 "
           pdb=" C2    C B  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   34.02  165.98     1      1.50e+01 4.44e-03 8.41e+01
  dihedral pdb=" O4'   C B  83 "
           pdb=" C1'   C B  83 "
           pdb=" N1    C B  83 "
           pdb=" C2    C B  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   65.45  166.55     1      1.70e+01 3.46e-03 6.55e+01
  dihedral pdb=" O4'   U B  96 "
           pdb=" C1'   U B  96 "
           pdb=" N1    U B  96 "
           pdb=" C2    U B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   36.49 -164.49     1      1.70e+01 3.46e-03 6.52e+01
  ... (remaining 6106 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1222
       0.094 -    0.188: 191
       0.188 -    0.282: 1
       0.282 -    0.376: 0
       0.376 -    0.470: 4
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" P     U C  11 "
            pdb=" OP1   U C  11 "
            pdb=" OP2   U C  11 "
            pdb=" O5'   U C  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.88   -0.47 2.00e-01 2.50e+01 5.53e+00
  chirality pdb=" P     C C   8 "
            pdb=" OP1   C C   8 "
            pdb=" OP2   C C   8 "
            pdb=" O5'   C C   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.86   -0.45 2.00e-01 2.50e+01 5.00e+00
  chirality pdb=" P     C C  10 "
            pdb=" OP1   C C  10 "
            pdb=" OP2   C C  10 "
            pdb=" O5'   C C  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.85   -0.44 2.00e-01 2.50e+01 4.77e+00
  ... (remaining 1415 not shown)

  Planarity restraints: 1147
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  80 "    0.029 2.00e-02 2.50e+03   1.15e-02 4.61e+00
        pdb=" N9    G B  80 "   -0.029 2.00e-02 2.50e+03
        pdb=" C8    G B  80 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G B  80 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    G B  80 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B  80 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6    G B  80 "    0.009 2.00e-02 2.50e+03
        pdb=" N1    G B  80 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G B  80 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B  80 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    G B  80 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G B  80 "   -0.004 2.00e-02 2.50e+03
        pdb=" H8    G B  80 "   -0.000 2.00e-02 2.50e+03
        pdb=" H1    G B  80 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B 203 "    0.024 2.00e-02 2.50e+03   1.06e-02 3.66e+00
        pdb=" N9    A B 203 "   -0.029 2.00e-02 2.50e+03
        pdb=" C8    A B 203 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A B 203 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    A B 203 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A B 203 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A B 203 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A B 203 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A B 203 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A B 203 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A B 203 "    0.001 2.00e-02 2.50e+03
        pdb=" H8    A B 203 "    0.000 2.00e-02 2.50e+03
        pdb=" H2    A B 203 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  56 "   -0.025 2.00e-02 2.50e+03   1.06e-02 3.65e+00
        pdb=" N9    A B  56 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    A B  56 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A B  56 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A B  56 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A B  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A B  56 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    A B  56 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    A B  56 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    A B  56 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A B  56 "    0.003 2.00e-02 2.50e+03
        pdb=" H8    A B  56 "   -0.001 2.00e-02 2.50e+03
        pdb=" H2    A B  56 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1144 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.40: 4446
        2.40 -     2.95: 22721
        2.95 -     3.50: 30862
        3.50 -     4.05: 44914
        4.05 -     4.60: 60404
  Nonbonded interactions: 163347
  Sorted by model distance:
  nonbonded pdb="HO2'   A B  86 "
            pdb=" H2'   C B  87 "
     model   vdw
     1.852 2.270
  nonbonded pdb=" H2'   A B   2 "
            pdb=" H8    A B   3 "
     model   vdw
     1.865 2.270
  nonbonded pdb=" HD1 PHE A 152 "
            pdb="HO2'   U C   7 "
     model   vdw
     1.870 2.100
  nonbonded pdb=" H2'   G B  40 "
            pdb=" H8    A B  41 "
     model   vdw
     1.870 2.270
  nonbonded pdb=" H   VAL A 394 "
            pdb=" H   ALA A 395 "
     model   vdw
     1.899 2.100
  ... (remaining 163342 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 individual isotropic
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:             2.320
  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:             0.060
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.650
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
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      :  0.004   0.037   7566  Z= 0.386
  Angle     :  0.755   7.392  11208  Z= 0.634
  Chirality :  0.056   0.470   1418
  Planarity :  0.004   0.036    673
  Dihedral  : 22.242 166.546   4166
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  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:  0.06 (0.50), residues: 330
  helix:  2.06 (0.54), residues: 112
  sheet: -1.98 (0.73), residues: 49
  loop : -0.69 (0.50), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 115 
 TYR   0.011   0.001   TYR A   5 
 PHE   0.008   0.001   PHE A  79 
 TRP   0.005   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00424 /  0.39 ( 7566)
  covalent geometry    : angle       0.75484 /  0.63 (11208)
  hydrogen bonds       : bond        0.11078 /  7.43 (  284)
  hydrogen bonds       : angle       4.51414 /  3.31 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.8531 (ttp80) cc_final: 0.7924 (ttp80)
REVERT: A   36 GLU cc_start: 0.7914 (tt0) cc_final: 0.7699 (tt0)
REVERT: A   69 SER cc_start: 0.8968 (t) cc_final: 0.8483 (m)
REVERT: A  179 LYS cc_start: 0.8214 (tppp) cc_final: 0.7714 (ttpt)
REVERT: A  339 HIS cc_start: 0.6737 (t70) cc_final: 0.6365 (t-170)
REVERT: A  342 ASP cc_start: 0.8515 (m-30) cc_final: 0.8189 (m-30)
REVERT: A  386 SER cc_start: 0.8523 (m) cc_final: 0.8143 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.8920
  time to fit residues: 72.5039
Evaluate side-chains
  51 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:   20.0000
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.9582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.115382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.072326 restraints weight = 28268.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.48
r_work: 0.2964 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7566  Z= 0.143
  Angle     :  0.503   6.464  11208  Z= 0.297
  Chirality :  0.035   0.228   1418
  Planarity :  0.004   0.034    673
  Dihedral  : 23.222 168.688   3482
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.76 %
    Favored  : 87.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.49), residues: 330
  helix:  2.16 (0.53), residues: 113
  sheet: -1.77 (0.73), residues: 49
  loop : -0.62 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 146 
 TYR   0.011   0.001   TYR A   5 
 PHE   0.007   0.001   PHE A  79 
 TRP   0.005   0.001   TRP A 161 
 HIS   0.005   0.001   HIS A  22 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.14 ( 7566)
  covalent geometry    : angle       0.50344 /  0.30 (11208)
  hydrogen bonds       : bond        0.05886 /  3.91 (  284)
  hydrogen bonds       : angle       3.71420 /  2.76 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.8276 (tpt) cc_final: 0.7998 (tpt)
REVERT: A   50 GLU cc_start: 0.8359 (pm20) cc_final: 0.7933 (mp0)
REVERT: A   68 MET cc_start: 0.8061 (mtt) cc_final: 0.7279 (mtt)
REVERT: A   69 SER cc_start: 0.8809 (t) cc_final: 0.8313 (m)
REVERT: A  179 LYS cc_start: 0.8300 (tppp) cc_final: 0.7636 (ttpt)
REVERT: A  332 GLU cc_start: 0.8335 (tt0) cc_final: 0.8093 (tm-30)
REVERT: A  339 HIS cc_start: 0.6727 (t70) cc_final: 0.6294 (t-170)
REVERT: A  342 ASP cc_start: 0.8499 (m-30) cc_final: 0.8181 (m-30)
REVERT: A  386 SER cc_start: 0.8381 (m) cc_final: 0.8073 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 60
  average time/residue: 0.9160
  time to fit residues: 58.2898
Evaluate side-chains
  54 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 4 optimal weight:    0.1980
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.2982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.114815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.071691 restraints weight = 28514.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.48
r_work: 0.2944 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7566  Z= 0.168
  Angle     :  0.499   6.581  11208  Z= 0.298
  Chirality :  0.034   0.241   1418
  Planarity :  0.004   0.037    673
  Dihedral  : 23.142 169.356   3482
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.15 %
    Favored  : 85.47 %
  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:  0.30 (0.49), residues: 330
  helix:  2.18 (0.53), residues: 113
  sheet: -1.79 (0.71), residues: 49
  loop : -0.51 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 115 
 TYR   0.011   0.001   TYR A   5 
 PHE   0.009   0.001   PHE A  79 
 TRP   0.004   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A 416 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.17 ( 7566)
  covalent geometry    : angle       0.49873 /  0.30 (11208)
  hydrogen bonds       : bond        0.05397 /  3.62 (  284)
  hydrogen bonds       : angle       3.40854 /  2.52 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 MET cc_start: 0.8271 (tpt) cc_final: 0.7939 (tpt)
REVERT: A   68 MET cc_start: 0.8083 (mtt) cc_final: 0.7223 (mtt)
REVERT: A   69 SER cc_start: 0.8847 (t) cc_final: 0.8347 (m)
REVERT: A  179 LYS cc_start: 0.8326 (tppp) cc_final: 0.7655 (ttpm)
REVERT: A  332 GLU cc_start: 0.8526 (tt0) cc_final: 0.8268 (tm-30)
REVERT: A  339 HIS cc_start: 0.6704 (t70) cc_final: 0.6297 (t-170)
REVERT: A  342 ASP cc_start: 0.8506 (m-30) cc_final: 0.8215 (m-30)
  outliers start: 4
  outliers final: 3
  residues processed: 60
  average time/residue: 0.8855
  time to fit residues: 56.3094
Evaluate side-chains
  54 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0470
   chunk 47 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.3284

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.114684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.071550 restraints weight = 28405.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 1.48
r_work: 0.2947 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7566  Z= 0.166
  Angle     :  0.496   6.685  11208  Z= 0.293
  Chirality :  0.034   0.242   1418
  Planarity :  0.004   0.039    673
  Dihedral  : 23.131 169.424   3482
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.80 %
    Favored  : 85.12 %
  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:  0.19 (0.49), residues: 330
  helix:  1.92 (0.51), residues: 119
  sheet: -1.74 (0.70), residues: 49
  loop : -0.59 (0.51), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 115 
 TYR   0.011   0.002   TYR A   5 
 PHE   0.008   0.001   PHE A  79 
 TRP   0.005   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A 339 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.17 ( 7566)
  covalent geometry    : angle       0.49616 /  0.29 (11208)
  hydrogen bonds       : bond        0.05230 /  3.52 (  284)
  hydrogen bonds       : angle       3.31667 /  2.47 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8356 (pm20) cc_final: 0.7969 (mp0)
REVERT: A   68 MET cc_start: 0.8127 (mtt) cc_final: 0.7292 (mtt)
REVERT: A   69 SER cc_start: 0.8905 (t) cc_final: 0.8393 (m)
REVERT: A  179 LYS cc_start: 0.8340 (tppp) cc_final: 0.7664 (ttpm)
REVERT: A  332 GLU cc_start: 0.8634 (tt0) cc_final: 0.8359 (tm-30)
REVERT: A  339 HIS cc_start: 0.6714 (t70) cc_final: 0.6400 (t-170)
REVERT: A  342 ASP cc_start: 0.8611 (m-30) cc_final: 0.8305 (m-30)
  outliers start: 6
  outliers final: 4
  residues processed: 59
  average time/residue: 0.9212
  time to fit residues: 57.2851
Evaluate side-chains
  58 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0170
   chunk 13 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.3022

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.114727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.071734 restraints weight = 28562.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.48
r_work: 0.2944 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7566  Z= 0.164
  Angle     :  0.489   6.651  11208  Z= 0.290
  Chirality :  0.034   0.243   1418
  Planarity :  0.004   0.040    673
  Dihedral  : 23.122 169.445   3482
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.49 %
    Favored  : 85.12 %
  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:  0.20 (0.49), residues: 330
  helix:  1.89 (0.51), residues: 121
  sheet: -1.66 (0.71), residues: 49
  loop : -0.60 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 115 
 TYR   0.015   0.002   TYR A 340 
 PHE   0.009   0.001   PHE A  79 
 TRP   0.005   0.001   TRP A 161 
 HIS   0.001   0.001   HIS A 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.16 ( 7566)
  covalent geometry    : angle       0.48856 /  0.29 (11208)
  hydrogen bonds       : bond        0.05128 /  3.44 (  284)
  hydrogen bonds       : angle       3.21056 /  2.38 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.8815 (mtp180) cc_final: 0.8457 (mtp180)
REVERT: A   69 SER cc_start: 0.8895 (t) cc_final: 0.8351 (m)
REVERT: A  179 LYS cc_start: 0.8335 (tppp) cc_final: 0.7654 (ttpm)
REVERT: A  332 GLU cc_start: 0.8696 (tt0) cc_final: 0.8400 (tm-30)
REVERT: A  339 HIS cc_start: 0.6779 (t70) cc_final: 0.6436 (t-170)
REVERT: A  342 ASP cc_start: 0.8523 (m-30) cc_final: 0.8243 (m-30)
  outliers start: 4
  outliers final: 4
  residues processed: 53
  average time/residue: 0.9380
  time to fit residues: 52.5463
Evaluate side-chains
  54 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.113697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.070494 restraints weight = 28638.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 1.49
r_work: 0.2920 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7566  Z= 0.217
  Angle     :  0.524   6.644  11208  Z= 0.308
  Chirality :  0.036   0.245   1418
  Planarity :  0.005   0.040    673
  Dihedral  : 23.102 168.846   3482
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.46 %
    Favored  : 85.81 %
  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 (0.49), residues: 330
  helix:  2.07 (0.52), residues: 115
  sheet: -1.67 (0.71), residues: 49
  loop : -0.48 (0.51), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  97 
 TYR   0.014   0.002   TYR A   5 
 PHE   0.010   0.001   PHE A  79 
 TRP   0.004   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A 399 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.22 ( 7566)
  covalent geometry    : angle       0.52363 /  0.31 (11208)
  hydrogen bonds       : bond        0.05347 /  3.56 (  284)
  hydrogen bonds       : angle       3.21743 /  2.38 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8415 (pm20) cc_final: 0.8140 (mp0)
REVERT: A   68 MET cc_start: 0.8190 (mtt) cc_final: 0.7831 (mmm)
REVERT: A   69 SER cc_start: 0.8920 (t) cc_final: 0.8302 (m)
REVERT: A  179 LYS cc_start: 0.8320 (tppp) cc_final: 0.7635 (ttpm)
REVERT: A  294 HIS cc_start: 0.4799 (OUTLIER) cc_final: 0.4521 (m170)
REVERT: A  338 ASP cc_start: 0.7983 (t0) cc_final: 0.7538 (t0)
REVERT: A  342 ASP cc_start: 0.8556 (m-30) cc_final: 0.8261 (m-30)
  outliers start: 5
  outliers final: 4
  residues processed: 56
  average time/residue: 0.9087
  time to fit residues: 53.8081
Evaluate side-chains
  55 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 50 optimal weight:   20.0000
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.9988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.113200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.069896 restraints weight = 28343.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 1.48
r_work: 0.2903 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7566  Z= 0.230
  Angle     :  0.533   6.623  11208  Z= 0.313
  Chirality :  0.036   0.246   1418
  Planarity :  0.005   0.040    673
  Dihedral  : 23.122 168.620   3482
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.19 %
    Favored  : 84.08 %
  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:  0.29 (0.49), residues: 330
  helix:  2.05 (0.51), residues: 115
  sheet: -1.68 (0.72), residues: 49
  loop : -0.49 (0.51), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  97 
 TYR   0.023   0.002   TYR A 340 
 PHE   0.010   0.001   PHE A  79 
 TRP   0.004   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A 399 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.23 ( 7566)
  covalent geometry    : angle       0.53323 /  0.31 (11208)
  hydrogen bonds       : bond        0.05362 /  3.56 (  284)
  hydrogen bonds       : angle       3.22446 /  2.38 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.8835 (mtp180) cc_final: 0.8598 (mtp180)
REVERT: A   50 GLU cc_start: 0.8413 (pm20) cc_final: 0.7992 (mp0)
REVERT: A   68 MET cc_start: 0.8266 (mtt) cc_final: 0.7924 (mmm)
REVERT: A   69 SER cc_start: 0.8961 (t) cc_final: 0.8335 (m)
REVERT: A  179 LYS cc_start: 0.8350 (tppp) cc_final: 0.7654 (ttpm)
REVERT: A  294 HIS cc_start: 0.4729 (OUTLIER) cc_final: 0.4487 (m170)
REVERT: A  312 ASP cc_start: 0.8565 (t0) cc_final: 0.8302 (t0)
REVERT: A  338 ASP cc_start: 0.8018 (t0) cc_final: 0.7581 (t0)
REVERT: A  342 ASP cc_start: 0.8552 (m-30) cc_final: 0.8287 (m-30)
  outliers start: 5
  outliers final: 4
  residues processed: 57
  average time/residue: 0.9068
  time to fit residues: 54.5860
Evaluate side-chains
  58 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 50 optimal weight:   20.0000
   chunk 35 optimal weight:    7.9990
   chunk 17 optimal weight:    0.3980
   chunk 18 optimal weight:    0.6980
   overall best weight:    1.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.113608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.070424 restraints weight = 28326.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.46
r_work: 0.2915 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7566  Z= 0.198
  Angle     :  0.520   6.627  11208  Z= 0.307
  Chirality :  0.036   0.245   1418
  Planarity :  0.005   0.039    673
  Dihedral  : 23.140 168.842   3482
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.84 %
    Favored  : 84.43 %
  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:  0.32 (0.49), residues: 330
  helix:  2.05 (0.51), residues: 115
  sheet: -1.63 (0.72), residues: 49
  loop : -0.48 (0.50), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 146 
 TYR   0.013   0.001   TYR A   5 
 PHE   0.008   0.001   PHE A  79 
 TRP   0.004   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A 399 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.20 ( 7566)
  covalent geometry    : angle       0.52015 /  0.31 (11208)
  hydrogen bonds       : bond        0.05267 /  3.50 (  284)
  hydrogen bonds       : angle       3.18700 /  2.35 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.8794 (mtp180) cc_final: 0.8581 (mtm-85)
REVERT: A   50 GLU cc_start: 0.8430 (pm20) cc_final: 0.8007 (mp0)
REVERT: A   68 MET cc_start: 0.8232 (mtt) cc_final: 0.7977 (mmm)
REVERT: A   69 SER cc_start: 0.8950 (t) cc_final: 0.8305 (m)
REVERT: A  179 LYS cc_start: 0.8312 (tppp) cc_final: 0.7618 (ttpm)
REVERT: A  294 HIS cc_start: 0.4689 (OUTLIER) cc_final: 0.4450 (m170)
REVERT: A  338 ASP cc_start: 0.8010 (t0) cc_final: 0.7549 (t0)
REVERT: A  342 ASP cc_start: 0.8532 (m-30) cc_final: 0.8265 (m-30)
  outliers start: 5
  outliers final: 4
  residues processed: 57
  average time/residue: 1.0912
  time to fit residues: 65.4799
Evaluate side-chains
  59 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.113775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.070582 restraints weight = 28250.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 1.47
r_work: 0.2926 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7566  Z= 0.174
  Angle     :  0.510   6.599  11208  Z= 0.303
  Chirality :  0.035   0.244   1418
  Planarity :  0.004   0.039    673
  Dihedral  : 23.150 168.970   3482
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.84 %
    Favored  : 84.43 %
  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:  0.23 (0.49), residues: 330
  helix:  1.85 (0.50), residues: 121
  sheet: -1.63 (0.72), residues: 49
  loop : -0.54 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 115 
 TYR   0.013   0.001   TYR A   5 
 PHE   0.007   0.001   PHE A  79 
 TRP   0.004   0.001   TRP A 161 
 HIS   0.001   0.001   HIS A 333 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.17 ( 7566)
  covalent geometry    : angle       0.51028 /  0.30 (11208)
  hydrogen bonds       : bond        0.05211 /  3.47 (  284)
  hydrogen bonds       : angle       3.16571 /  2.34 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.8827 (mtp180) cc_final: 0.8614 (mtm-85)
REVERT: A   50 GLU cc_start: 0.8415 (pm20) cc_final: 0.7997 (mp0)
REVERT: A   68 MET cc_start: 0.8247 (mtt) cc_final: 0.8003 (mmm)
REVERT: A   69 SER cc_start: 0.8960 (t) cc_final: 0.8325 (m)
REVERT: A  179 LYS cc_start: 0.8348 (tppp) cc_final: 0.7651 (ttpm)
REVERT: A  294 HIS cc_start: 0.4738 (OUTLIER) cc_final: 0.4492 (m170)
REVERT: A  338 ASP cc_start: 0.8008 (t0) cc_final: 0.7557 (t0)
REVERT: A  342 ASP cc_start: 0.8552 (m-30) cc_final: 0.8286 (m-30)
  outliers start: 5
  outliers final: 4
  residues processed: 57
  average time/residue: 1.0325
  time to fit residues: 62.0534
Evaluate side-chains
  59 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 40 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.113639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.070790 restraints weight = 28534.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.46
r_work: 0.2914 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7566  Z= 0.203
  Angle     :  0.517   6.629  11208  Z= 0.305
  Chirality :  0.036   0.246   1418
  Planarity :  0.005   0.040    673
  Dihedral  : 23.137 169.141   3482
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.84 %
    Favored  : 84.43 %
  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:  0.29 (0.49), residues: 330
  helix:  1.89 (0.50), residues: 121
  sheet: -1.57 (0.72), residues: 49
  loop : -0.51 (0.51), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  97 
 TYR   0.025   0.002   TYR A 340 
 PHE   0.009   0.001   PHE A  79 
 TRP   0.004   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A 399 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.20 ( 7566)
  covalent geometry    : angle       0.51740 /  0.31 (11208)
  hydrogen bonds       : bond        0.05203 /  3.44 (  284)
  hydrogen bonds       : angle       3.14610 /  2.32 (  623)

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

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

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  660 Ramachandran restraints generated.
    330 Oldfield, 0 Emsley, 330 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8620 (mtm-85)
REVERT: A   50 GLU cc_start: 0.8403 (pm20) cc_final: 0.7994 (mp0)
REVERT: A  179 LYS cc_start: 0.8304 (tppp) cc_final: 0.7779 (ttpp)
REVERT: A  294 HIS cc_start: 0.4732 (OUTLIER) cc_final: 0.4507 (m170)
REVERT: A  309 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8579 (mp10)
REVERT: A  312 ASP cc_start: 0.8549 (t0) cc_final: 0.8282 (t0)
REVERT: A  338 ASP cc_start: 0.7997 (t0) cc_final: 0.7532 (t0)
REVERT: A  342 ASP cc_start: 0.8561 (m-30) cc_final: 0.8283 (m-30)
REVERT: A  411 GLU cc_start: 0.8702 (mp0) cc_final: 0.8500 (mp0)
  outliers start: 5
  outliers final: 4
  residues processed: 56
  average time/residue: 1.0051
  time to fit residues: 59.1452
Evaluate side-chains
  54 residues out of total 289 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  378 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0670
   chunk 51 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    2.4126

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 369 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.111902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.069520 restraints weight = 28465.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 1.45
r_work: 0.2867 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7566  Z= 0.281
  Angle     :  0.572   6.550  11208  Z= 0.332
  Chirality :  0.038   0.257   1418
  Planarity :  0.005   0.040    673
  Dihedral  : 23.124 168.780   3482
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.19 %
    Favored  : 84.08 %
  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 (0.48), residues: 330
  helix:  1.84 (0.49), residues: 119
  sheet: -1.64 (0.71), residues: 49
  loop : -0.58 (0.51), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  97 
 TYR   0.023   0.002   TYR A 340 
 PHE   0.011   0.002   PHE A  79 
 TRP   0.003   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 168 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00505 /  0.28 ( 7566)
  covalent geometry    : angle       0.57158 /  0.33 (11208)
  hydrogen bonds       : bond        0.05703 /  3.75 (  284)
  hydrogen bonds       : angle       3.24982 /  2.39 (  623)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5244.00 seconds
wall clock time: 89 minutes 11.60 seconds (5351.60 seconds total)