Starting phenix.real_space_refine
on Tue Feb 11 08:35:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p2q_13172/02_2025/7p2q_13172_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p2q_13172/02_2025/7p2q_13172.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p2q_13172/02_2025/7p2q_13172.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p2q_13172/02_2025/7p2q_13172.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p2q_13172/02_2025/7p2q_13172_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p2q_13172/02_2025/7p2q_13172_neut.cif"
  }
  resolution = 4.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    3106      2.51       5
     N     778      2.21       5
     O     873      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4780
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1186
          Classifications: {'peptide': 148}
          Link IDs: {'PTRANS': 6, 'TRANS': 141}
    Chain: "B"
      Number of atoms: 1426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1426
          Classifications: {'peptide': 179}
          Link IDs: {'PTRANS': 7, 'TRANS': 171}
    Chain: "C"
      Number of atoms: 1411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1411
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 6, 'TRANS': 167}
    Chain: "D"
      Number of atoms: 696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 696
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 6, 'TRANS': 79}
    Chain: "E"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 3.33, per 1000 atoms: 0.70
  Number of scatterers: 4780
  At special positions: 0
  Unit cell: (81.81, 84.24, 126.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O     873      8.00
     N     778      7.00
     C    3106      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
    ALPHA1-6
      " BMA E   3 " - " MAN E   5 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG E   1 " - " ASN B 141 "
  Time building additional restraints: 1.44
  Conformation dependent library (CDL) restraints added in 562.2 milliseconds
  

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1102

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 6 sheets defined
      41.4% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 56
      removed outlier: 4.288A  pdb=" N   LEU A  30 " --> pdb=" O   ASN A  26 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   GLY A  56 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 171
      removed outlier: 3.782A  pdb=" N   VAL A 164 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   TYR A 171 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 33
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 79 through 105
    Processing helix  chain 'C' and resid 106 through 109
      removed outlier: 3.516A  pdb=" N   GLU C 109 " --> pdb=" O   PRO C 106 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 106 through 109'
    Processing helix  chain 'C' and resid 110 through 136
      removed outlier: 3.720A  pdb=" N   LEU C 114 " --> pdb=" O   SER C 110 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS C 135 " --> pdb=" O   TYR C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 196
      No H-bonds generated for 'chain 'C' and resid 194 through 196'
    Processing helix  chain 'C' and resid 207 through 224
      removed outlier: 3.700A  pdb=" N   GLU C 211 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 73
      removed outlier: 3.653A  pdb=" N   LEU D  72 " --> pdb=" O   MET D  68 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   SER D  73 " --> pdb=" O   LEU D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 109
    Processing helix  chain 'D' and resid 112 through 131
    Processing helix  chain 'D' and resid 135 through 140
    Processing helix  chain 'D' and resid 140 through 145
      removed outlier: 3.601A  pdb=" N   LEU D 145 " --> pdb=" O   PRO D 141 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64
      removed outlier: 3.983A  pdb=" N   ASP A  77 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99
      removed outlier: 5.282A  pdb=" N   VAL A 110 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LYS A 126 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LYS A 112 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55
      removed outlier: 4.094A  pdb=" N   VAL B  51 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LEU B  63 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   ASP B  53 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   SER B  61 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE B 129 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 108 through 111
      removed outlier: 3.679A  pdb=" N   GLN B  84 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104
    Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 76
      removed outlier: 6.622A  pdb=" N   LEU C 159 " --> pdb=" O   PHE C 140 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   VAL C 142 " --> pdb=" O   TRP C 157 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   TRP C 157 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)

    241 hydrogen bonds defined for protein.
    693 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1460
        1.34 -     1.46: 971
        1.46 -     1.58: 2424
        1.58 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 4896
  Sorted by residual:
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.567 -0.048 2.00e-02 2.50e+03 5.76e+00
  bond pdb=" C1  MAN E   4 "
       pdb=" C2  MAN E   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.563 -0.037 2.00e-02 2.50e+03 3.45e+00
  bond pdb=" C1  BMA E   3 "
       pdb=" O5  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.410  1.445 -0.035 2.00e-02 2.50e+03 2.99e+00
  bond pdb=" C5  MAN E   4 "
       pdb=" O5  MAN E   4 "
    ideal  model  delta    sigma   weight residual
    1.418  1.452 -0.034 2.00e-02 2.50e+03 2.94e+00
  bond pdb=" C   LEU D 131 "
       pdb=" N   PRO D 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.18e-02 7.18e+03 2.88e+00
  ... (remaining 4891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 6412
        1.91 -     3.81: 165
        3.81 -     5.72: 31
        5.72 -     7.63: 15
        7.63 -     9.53: 6
  Bond angle restraints: 6629
  Sorted by residual:
  angle pdb=" C   LYS B 121 "
        pdb=" N   ASP B 122 "
        pdb=" CA  ASP B 122 "
      ideal   model   delta    sigma   weight residual
     121.54  131.00   -9.46 1.91e+00 2.74e-01 2.45e+01
  angle pdb=" C   GLY B 133 "
        pdb=" N   ASN B 134 "
        pdb=" CA  ASN B 134 "
      ideal   model   delta    sigma   weight residual
     121.54  130.70   -9.16 1.91e+00 2.74e-01 2.30e+01
  angle pdb=" C   GLU A  58 "
        pdb=" N   SER A  59 "
        pdb=" CA  SER A  59 "
      ideal   model   delta    sigma   weight residual
     121.80  130.19   -8.39 2.44e+00 1.68e-01 1.18e+01
  angle pdb=" N   SER A  59 "
        pdb=" CA  SER A  59 "
        pdb=" C   SER A  59 "
      ideal   model   delta    sigma   weight residual
     109.81  116.82   -7.01 2.21e+00 2.05e-01 1.00e+01
  angle pdb=" CA  LEU D  75 "
        pdb=" CB  LEU D  75 "
        pdb=" CG  LEU D  75 "
      ideal   model   delta    sigma   weight residual
     116.30  125.83   -9.53 3.50e+00 8.16e-02 7.42e+00
  ... (remaining 6624 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.22: 2892
       21.22 -    42.44: 61
       42.44 -    63.66: 4
       63.66 -    84.89: 7
       84.89 -   106.11: 4
  Dihedral angle restraints: 2968
    sinusoidal: 1260
      harmonic: 1708
  Sorted by residual:
  dihedral pdb=" CA  ASP C 154 "
           pdb=" C   ASP C 154 "
           pdb=" N   ASP C 155 "
           pdb=" CA  ASP C 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  TYR B 174 "
           pdb=" C   TYR B 174 "
           pdb=" N   GLU B 175 "
           pdb=" CA  GLU B 175 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.01  -18.99     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" O4  BMA E   3 "
           pdb=" C4  BMA E   3 "
           pdb=" C5  BMA E   3 "
           pdb=" O5  BMA E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.40  106.11     1      3.00e+01 1.11e-03 1.36e+01
  ... (remaining 2965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 590
       0.057 -    0.114: 138
       0.114 -    0.171: 22
       0.171 -    0.228: 5
       0.228 -    0.285: 1
  Chirality restraints: 756
  Sorted by residual:
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CB  ILE B 109 "
            pdb=" CA  ILE B 109 "
            pdb=" CG1 ILE B 109 "
            pdb=" CG2 ILE B 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  ASN B 134 "
            pdb=" N   ASN B 134 "
            pdb=" C   ASN B 134 "
            pdb=" CB  ASN B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 753 not shown)

  Planarity restraints: 822
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D 140 "   -0.038 5.00e-02 4.00e+02   5.70e-02 5.20e+00
        pdb=" N   PRO D 141 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO D 141 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO D 141 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  70 "    0.033 5.00e-02 4.00e+02   4.93e-02 3.88e+00
        pdb=" N   PRO A  71 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A  71 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  71 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  37 "   -0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO B  38 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B  38 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  38 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 819 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1005
        2.79 -     3.32: 4108
        3.32 -     3.85: 7306
        3.85 -     4.37: 7850
        4.37 -     4.90: 13680
  Nonbonded interactions: 33949
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 109 "
            pdb=" CE1 PHE B  86 "
     model   vdw
     2.264 3.420
  nonbonded pdb=" O   LYS B 121 "
            pdb=" OD1 ASP B 122 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NH1 ARG C  84 "
            pdb=" OE2 GLU C 136 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OG  SER B  90 "
            pdb=" O   THR B 145 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" OD1 ASP A 120 "
            pdb=" NZ  LYS A 147 "
     model   vdw
     2.401 3.120
  ... (remaining 33944 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:             0.810
  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:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.250
  Find NCS groups from input model:        0.050
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
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   0.048   4896  Z= 0.243
  Angle     :  0.840   9.532   6629  Z= 0.432
  Chirality :  0.051   0.285    756
  Planarity :  0.007   0.057    821
  Dihedral  : 11.107 106.107   1866
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.09 (0.29), residues: 579
  helix: -1.26 (0.24), residues: 220
  sheet: -1.18 (0.47), residues: 120
  loop : -3.26 (0.32), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 157 
 HIS   0.009   0.002   HIS C 144 
 PHE   0.024   0.002   PHE A  80 
 TYR   0.023   0.002   TYR B 174 
 ARG   0.005   0.000   ARG B 112 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 TYR cc_start: 0.8489 (m-10) cc_final: 0.7727 (m-80)
REVERT: A   47 ILE cc_start: 0.8986 (mt) cc_final: 0.8784 (mt)
REVERT: A   52 ILE cc_start: 0.8925 (pt) cc_final: 0.8577 (pt)
REVERT: A   90 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7112 (mmt90)
REVERT: A  134 ASP cc_start: 0.8211 (m-30) cc_final: 0.7242 (t0)
REVERT: A  146 GLU cc_start: 0.6990 (tt0) cc_final: 0.6722 (tt0)
REVERT: A  158 LEU cc_start: 0.8953 (mm) cc_final: 0.8742 (mm)
REVERT: B   42 HIS cc_start: 0.8714 (m-70) cc_final: 0.8397 (t-170)
REVERT: B   49 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7918 (ptpp)
REVERT: B   59 GLU cc_start: 0.7296 (tp30) cc_final: 0.6952 (tp30)
REVERT: B   73 ASP cc_start: 0.8255 (t0) cc_final: 0.7370 (t70)
REVERT: B   78 PHE cc_start: 0.7880 (m-80) cc_final: 0.7513 (m-80)
REVERT: B   80 TRP cc_start: 0.6359 (m100) cc_final: 0.5855 (p-90)
REVERT: B  128 PHE cc_start: 0.7994 (m-10) cc_final: 0.7730 (m-10)
REVERT: C   70 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8536 (tm-30)
REVERT: C  102 ASP cc_start: 0.8659 (m-30) cc_final: 0.8314 (m-30)
REVERT: C  174 LEU cc_start: 0.8449 (mm) cc_final: 0.7380 (mm)
REVERT: C  208 TYR cc_start: 0.9118 (t80) cc_final: 0.8689 (t80)
REVERT: D   68 MET cc_start: 0.9152 (mtt) cc_final: 0.8800 (tmm)
REVERT: D  128 LEU cc_start: 0.8645 (mt) cc_final: 0.8394 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.2219
  time to fit residues: 71.1077
Evaluate side-chains
  153 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 105 HIS
** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 GLN ** 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 = 0.3648 r_free = 0.3648 target = 0.078929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.062844 restraints weight = 27233.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.064504 restraints weight = 21150.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.065536 restraints weight = 17343.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4896  Z= 0.209
  Angle     :  0.711   9.183   6629  Z= 0.360
  Chirality :  0.046   0.184    756
  Planarity :  0.006   0.060    821
  Dihedral  : 10.478  84.931    731
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.34 %
    Favored  : 98.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.33), residues: 579
  helix:  0.62 (0.31), residues: 220
  sheet: -0.74 (0.48), residues: 126
  loop : -2.81 (0.34), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 101 
 HIS   0.007   0.001   HIS C 144 
 PHE   0.018   0.002   PHE A  37 
 TYR   0.018   0.002   TYR C 208 
 ARG   0.006   0.001   ARG C 145 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.8981 (m-80) cc_final: 0.8652 (m-80)
REVERT: A   32 TYR cc_start: 0.8161 (m-10) cc_final: 0.7865 (m-80)
REVERT: A   33 GLN cc_start: 0.8995 (mm110) cc_final: 0.8615 (mm-40)
REVERT: A   46 MET cc_start: 0.7854 (ttp) cc_final: 0.7504 (ttp)
REVERT: A   51 LEU cc_start: 0.9481 (mt) cc_final: 0.9277 (mt)
REVERT: A  121 ILE cc_start: 0.6642 (mm) cc_final: 0.5816 (mm)
REVERT: A  134 ASP cc_start: 0.7567 (m-30) cc_final: 0.7366 (t0)
REVERT: A  146 GLU cc_start: 0.6850 (tt0) cc_final: 0.6545 (tt0)
REVERT: A  158 LEU cc_start: 0.9083 (mm) cc_final: 0.8502 (mm)
REVERT: B   42 HIS cc_start: 0.8734 (m-70) cc_final: 0.8435 (t-170)
REVERT: B   73 ASP cc_start: 0.8456 (t0) cc_final: 0.7614 (t70)
REVERT: B   80 TRP cc_start: 0.6361 (m100) cc_final: 0.5702 (p-90)
REVERT: C   94 PHE cc_start: 0.8640 (m-10) cc_final: 0.8335 (m-10)
REVERT: C  102 ASP cc_start: 0.8532 (m-30) cc_final: 0.8285 (m-30)
REVERT: C  174 LEU cc_start: 0.8132 (mm) cc_final: 0.7807 (mm)
REVERT: C  208 TYR cc_start: 0.9065 (t80) cc_final: 0.8790 (t80)
REVERT: D  131 LEU cc_start: 0.8884 (mt) cc_final: 0.8431 (mt)
REVERT: D  139 ARG cc_start: 0.8381 (ttt180) cc_final: 0.8041 (ptt180)
  outliers start: 1
  outliers final: 1
  residues processed: 192
  average time/residue: 0.1840
  time to fit residues: 43.2198
Evaluate side-chains
  138 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:   40.0000
   chunk 23 optimal weight:    0.0030
   chunk 41 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0030
   chunk 30 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0060
   chunk 26 optimal weight:    0.1980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.2216

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.079568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.062398 restraints weight = 27691.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.063869 restraints weight = 22155.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.065030 restraints weight = 18600.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.5161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4896  Z= 0.154
  Angle     :  0.664   7.868   6629  Z= 0.330
  Chirality :  0.045   0.196    756
  Planarity :  0.005   0.046    821
  Dihedral  :  9.510  74.344    731
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.34), residues: 579
  helix:  1.11 (0.33), residues: 226
  sheet: -0.14 (0.48), residues: 131
  loop : -2.82 (0.35), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 148 
 HIS   0.003   0.001   HIS C 199 
 PHE   0.016   0.001   PHE A  80 
 TYR   0.018   0.001   TYR C 121 
 ARG   0.003   0.000   ARG A 109 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.9085 (pm20) cc_final: 0.8862 (pm20)
REVERT: A   30 LEU cc_start: 0.9273 (tt) cc_final: 0.8918 (mp)
REVERT: A   32 TYR cc_start: 0.8278 (m-10) cc_final: 0.8019 (m-80)
REVERT: A   33 GLN cc_start: 0.9065 (mm110) cc_final: 0.8664 (mm-40)
REVERT: A   36 ASN cc_start: 0.9042 (m110) cc_final: 0.8776 (m-40)
REVERT: A   46 MET cc_start: 0.7912 (ttp) cc_final: 0.7439 (ttp)
REVERT: A   74 HIS cc_start: 0.8733 (m-70) cc_final: 0.8163 (m-70)
REVERT: A  121 ILE cc_start: 0.6803 (mm) cc_final: 0.6313 (mm)
REVERT: A  133 ASP cc_start: 0.6777 (t70) cc_final: 0.6332 (t70)
REVERT: A  134 ASP cc_start: 0.7576 (m-30) cc_final: 0.7246 (t0)
REVERT: A  146 GLU cc_start: 0.6754 (tt0) cc_final: 0.6465 (tt0)
REVERT: B   42 HIS cc_start: 0.8716 (m-70) cc_final: 0.8401 (t-170)
REVERT: B   47 MET cc_start: 0.6686 (tmm) cc_final: 0.6313 (tmm)
REVERT: B   73 ASP cc_start: 0.8554 (t0) cc_final: 0.8133 (m-30)
REVERT: B   80 TRP cc_start: 0.6238 (m100) cc_final: 0.5684 (p-90)
REVERT: B  102 GLN cc_start: 0.7217 (pm20) cc_final: 0.6641 (pm20)
REVERT: C   94 PHE cc_start: 0.8816 (m-10) cc_final: 0.8511 (m-10)
REVERT: C  102 ASP cc_start: 0.8478 (m-30) cc_final: 0.8235 (m-30)
REVERT: C  121 TYR cc_start: 0.8100 (t80) cc_final: 0.7783 (t80)
REVERT: C  162 SER cc_start: 0.8157 (t) cc_final: 0.7904 (t)
REVERT: C  167 ASP cc_start: 0.8296 (t0) cc_final: 0.7817 (t0)
REVERT: C  168 ASP cc_start: 0.8162 (t0) cc_final: 0.7737 (t0)
REVERT: C  193 ILE cc_start: 0.9203 (pt) cc_final: 0.8952 (mp)
REVERT: C  203 LEU cc_start: 0.8255 (tp) cc_final: 0.7996 (tp)
REVERT: C  208 TYR cc_start: 0.9032 (t80) cc_final: 0.8752 (t80)
REVERT: D   71 HIS cc_start: 0.7264 (m90) cc_final: 0.6855 (m-70)
REVERT: D  139 ARG cc_start: 0.8333 (ttt180) cc_final: 0.8009 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1666
  time to fit residues: 38.3338
Evaluate side-chains
  148 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 19 optimal weight:   20.0000
   chunk 41 optimal weight:    0.3980
   chunk 33 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 31 optimal weight:    0.6980
   chunk 28 optimal weight:   10.0000
   chunk 21 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0030
   chunk 3 optimal weight:    0.0020
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 144 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.079220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.062209 restraints weight = 27472.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.063768 restraints weight = 21753.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.065016 restraints weight = 18094.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.5426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4896  Z= 0.149
  Angle     :  0.659   8.692   6629  Z= 0.324
  Chirality :  0.045   0.212    756
  Planarity :  0.004   0.046    821
  Dihedral  :  8.688  63.841    731
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.35), residues: 579
  helix:  1.46 (0.34), residues: 226
  sheet: -0.23 (0.48), residues: 131
  loop : -2.65 (0.35), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 148 
 HIS   0.003   0.001   HIS C 216 
 PHE   0.012   0.001   PHE A  37 
 TYR   0.012   0.001   TYR B  88 
 ARG   0.003   0.000   ARG A 109 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.9071 (pm20) cc_final: 0.8816 (pm20)
REVERT: A   30 LEU cc_start: 0.9237 (tt) cc_final: 0.8864 (mp)
REVERT: A   32 TYR cc_start: 0.8252 (m-10) cc_final: 0.7975 (m-80)
REVERT: A   33 GLN cc_start: 0.9025 (mm110) cc_final: 0.8604 (mm-40)
REVERT: A   46 MET cc_start: 0.7899 (ttp) cc_final: 0.7414 (ttp)
REVERT: A  109 ARG cc_start: 0.7046 (ttt-90) cc_final: 0.6525 (ttt-90)
REVERT: A  121 ILE cc_start: 0.6977 (mm) cc_final: 0.6572 (mm)
REVERT: B   42 HIS cc_start: 0.8661 (m-70) cc_final: 0.8364 (t70)
REVERT: B   79 ASP cc_start: 0.8324 (m-30) cc_final: 0.6707 (p0)
REVERT: B   80 TRP cc_start: 0.6338 (m100) cc_final: 0.5851 (p-90)
REVERT: B  121 LYS cc_start: 0.8966 (mppt) cc_final: 0.8500 (mmtm)
REVERT: B  122 ASP cc_start: 0.8715 (p0) cc_final: 0.8452 (t0)
REVERT: C   94 PHE cc_start: 0.8551 (m-10) cc_final: 0.8191 (m-10)
REVERT: C  102 ASP cc_start: 0.8390 (m-30) cc_final: 0.8146 (m-30)
REVERT: C  124 MET cc_start: 0.7838 (ppp) cc_final: 0.7256 (ptt)
REVERT: C  167 ASP cc_start: 0.8249 (t0) cc_final: 0.7726 (t0)
REVERT: C  193 ILE cc_start: 0.9046 (pt) cc_final: 0.8690 (pt)
REVERT: C  197 PHE cc_start: 0.8699 (m-80) cc_final: 0.7915 (p90)
REVERT: C  203 LEU cc_start: 0.7977 (tp) cc_final: 0.7545 (tp)
REVERT: C  208 TYR cc_start: 0.8785 (t80) cc_final: 0.8576 (t80)
REVERT: D   71 HIS cc_start: 0.7295 (m90) cc_final: 0.7076 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1653
  time to fit residues: 37.5014
Evaluate side-chains
  146 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   chunk 7 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.077183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.060682 restraints weight = 26440.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.062200 restraints weight = 20842.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.063387 restraints weight = 17220.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.6011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4896  Z= 0.193
  Angle     :  0.660   8.486   6629  Z= 0.330
  Chirality :  0.045   0.180    756
  Planarity :  0.004   0.038    821
  Dihedral  :  7.929  55.352    731
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.35), residues: 579
  helix:  1.72 (0.35), residues: 226
  sheet: -0.11 (0.48), residues: 131
  loop : -2.48 (0.36), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 148 
 HIS   0.009   0.002   HIS D 140 
 PHE   0.019   0.002   PHE A  80 
 TYR   0.020   0.001   TYR B  88 
 ARG   0.007   0.000   ARG D 139 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TYR cc_start: 0.8932 (m-80) cc_final: 0.8609 (m-80)
REVERT: A   32 TYR cc_start: 0.8030 (m-10) cc_final: 0.7698 (m-80)
REVERT: A   33 GLN cc_start: 0.9010 (mm110) cc_final: 0.8543 (mm-40)
REVERT: A   46 MET cc_start: 0.7850 (ttp) cc_final: 0.7394 (ttp)
REVERT: A  112 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8620 (mmmm)
REVERT: A  121 ILE cc_start: 0.6964 (mm) cc_final: 0.6505 (mm)
REVERT: A  146 GLU cc_start: 0.6428 (tt0) cc_final: 0.5946 (tt0)
REVERT: B   49 LYS cc_start: 0.7184 (mtmm) cc_final: 0.6836 (mtmm)
REVERT: B  122 ASP cc_start: 0.8698 (p0) cc_final: 0.8479 (p0)
REVERT: C   94 PHE cc_start: 0.8590 (m-10) cc_final: 0.8234 (m-10)
REVERT: C  102 ASP cc_start: 0.8402 (m-30) cc_final: 0.8163 (m-30)
REVERT: C  124 MET cc_start: 0.7996 (ppp) cc_final: 0.7527 (ptt)
REVERT: C  166 PHE cc_start: 0.6966 (m-10) cc_final: 0.6108 (m-10)
REVERT: C  167 ASP cc_start: 0.8219 (t0) cc_final: 0.7650 (t0)
REVERT: C  168 ASP cc_start: 0.8444 (t0) cc_final: 0.8016 (t0)
REVERT: C  208 TYR cc_start: 0.8797 (t80) cc_final: 0.8449 (t80)
REVERT: D   71 HIS cc_start: 0.7196 (m90) cc_final: 0.6902 (m-70)
REVERT: D  139 ARG cc_start: 0.7484 (ppt170) cc_final: 0.7157 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1665
  time to fit residues: 36.3773
Evaluate side-chains
  137 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   chunk 43 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS
A 129 ASN
A 143 ASN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 102 GLN
C  58 ASN
C  77 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.072400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.057504 restraints weight = 28763.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.058772 restraints weight = 23171.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.059785 restraints weight = 19493.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.6718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4896  Z= 0.340
  Angle     :  0.789   8.435   6629  Z= 0.408
  Chirality :  0.048   0.178    756
  Planarity :  0.005   0.044    821
  Dihedral  :  7.217  54.386    731
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  1.92 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.35), residues: 579
  helix:  1.46 (0.34), residues: 219
  sheet: -0.30 (0.49), residues: 130
  loop : -2.31 (0.36), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 144 
 HIS   0.009   0.002   HIS C 216 
 PHE   0.019   0.002   PHE C  94 
 TYR   0.027   0.002   TYR B  88 
 ARG   0.011   0.001   ARG C 223 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 GLN cc_start: 0.8986 (pm20) cc_final: 0.8688 (pm20)
REVERT: A   32 TYR cc_start: 0.7959 (m-10) cc_final: 0.7638 (m-80)
REVERT: A   33 GLN cc_start: 0.9083 (mm110) cc_final: 0.8639 (mm110)
REVERT: A   69 MET cc_start: 0.9440 (mmm) cc_final: 0.9236 (mmm)
REVERT: A  121 ILE cc_start: 0.7307 (mm) cc_final: 0.6945 (mm)
REVERT: A  146 GLU cc_start: 0.6632 (tt0) cc_final: 0.6043 (tt0)
REVERT: A  158 LEU cc_start: 0.9340 (mm) cc_final: 0.8850 (mm)
REVERT: B   86 PHE cc_start: 0.8183 (m-80) cc_final: 0.7970 (m-80)
REVERT: B  122 ASP cc_start: 0.8768 (p0) cc_final: 0.8563 (p0)
REVERT: C  102 ASP cc_start: 0.8554 (m-30) cc_final: 0.8265 (m-30)
REVERT: C  124 MET cc_start: 0.8261 (ppp) cc_final: 0.7806 (ptm)
REVERT: C  188 GLU cc_start: 0.9057 (pp20) cc_final: 0.8738 (pp20)
REVERT: C  208 TYR cc_start: 0.8877 (t80) cc_final: 0.8557 (t80)
REVERT: D   68 MET cc_start: 0.8582 (mpp) cc_final: 0.8354 (tmm)
REVERT: D  139 ARG cc_start: 0.7556 (ppt170) cc_final: 0.6981 (ptt180)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1610
  time to fit residues: 32.1448
Evaluate side-chains
  127 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   chunk 42 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
** B  84 GLN ** 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 = 0.3514 r_free = 0.3514 target = 0.073162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.058649 restraints weight = 28543.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.059911 restraints weight = 22780.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.060952 restraints weight = 19146.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.6914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4896  Z= 0.236
  Angle     :  0.712   8.305   6629  Z= 0.361
  Chirality :  0.044   0.144    756
  Planarity :  0.004   0.043    821
  Dihedral  :  6.428  55.521    731
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.36), residues: 579
  helix:  1.63 (0.35), residues: 220
  sheet: -0.51 (0.47), residues: 136
  loop : -2.28 (0.38), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 134 
 HIS   0.006   0.002   HIS C 216 
 PHE   0.015   0.002   PHE C 197 
 TYR   0.011   0.002   TYR C 208 
 ARG   0.004   0.000   ARG B 112 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 TYR cc_start: 0.7955 (m-10) cc_final: 0.7730 (m-80)
REVERT: A   69 MET cc_start: 0.9423 (mmm) cc_final: 0.9205 (mmm)
REVERT: A  121 ILE cc_start: 0.7255 (mm) cc_final: 0.6929 (mm)
REVERT: A  146 GLU cc_start: 0.6461 (tt0) cc_final: 0.5807 (tt0)
REVERT: B  122 ASP cc_start: 0.8734 (p0) cc_final: 0.8513 (p0)
REVERT: C  102 ASP cc_start: 0.8493 (m-30) cc_final: 0.8220 (m-30)
REVERT: C  166 PHE cc_start: 0.6942 (m-10) cc_final: 0.6090 (m-10)
REVERT: C  174 LEU cc_start: 0.8647 (mm) cc_final: 0.8313 (mp)
REVERT: C  188 GLU cc_start: 0.9012 (pp20) cc_final: 0.8695 (pp20)
REVERT: C  208 TYR cc_start: 0.8832 (t80) cc_final: 0.8517 (t80)
REVERT: D   68 MET cc_start: 0.8644 (mpp) cc_final: 0.8282 (tmm)
REVERT: D  129 LEU cc_start: 0.8965 (mt) cc_final: 0.8653 (mt)
REVERT: D  139 ARG cc_start: 0.7492 (ppt170) cc_final: 0.6847 (ptt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1812
  time to fit residues: 37.0410
Evaluate side-chains
  127 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:    0.0970
   chunk 51 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 20 optimal weight:    8.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 111 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.074469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.059303 restraints weight = 28065.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.060684 restraints weight = 22218.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.061800 restraints weight = 18530.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.6942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4896  Z= 0.192
  Angle     :  0.729  11.475   6629  Z= 0.357
  Chirality :  0.045   0.178    756
  Planarity :  0.004   0.040    821
  Dihedral  :  6.206  55.893    731
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.36), residues: 579
  helix:  1.64 (0.35), residues: 222
  sheet: -0.51 (0.46), residues: 137
  loop : -2.22 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  80 
 HIS   0.003   0.001   HIS C 199 
 PHE   0.019   0.002   PHE C  94 
 TYR   0.015   0.001   TYR D 107 
 ARG   0.003   0.000   ARG A 109 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.576 
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   31 TYR cc_start: 0.8951 (m-80) cc_final: 0.8605 (m-80)
REVERT: A   69 MET cc_start: 0.9427 (mmm) cc_final: 0.9223 (mmm)
REVERT: A   79 LEU cc_start: 0.9354 (mm) cc_final: 0.9052 (mm)
REVERT: A  121 ILE cc_start: 0.7331 (mm) cc_final: 0.6993 (mm)
REVERT: A  128 ASP cc_start: 0.8850 (t0) cc_final: 0.8564 (t0)
REVERT: A  146 GLU cc_start: 0.6441 (tt0) cc_final: 0.5766 (tt0)
REVERT: A  158 LEU cc_start: 0.9337 (mm) cc_final: 0.8705 (mm)
REVERT: B   47 MET cc_start: 0.7450 (tmm) cc_final: 0.7145 (tmm)
REVERT: B   80 TRP cc_start: 0.6647 (m100) cc_final: 0.6338 (p-90)
REVERT: B  122 ASP cc_start: 0.8835 (p0) cc_final: 0.8619 (p0)
REVERT: C   90 ILE cc_start: 0.9098 (mt) cc_final: 0.8869 (mt)
REVERT: C  102 ASP cc_start: 0.8544 (m-30) cc_final: 0.8243 (m-30)
REVERT: C  166 PHE cc_start: 0.6845 (m-10) cc_final: 0.6031 (m-10)
REVERT: C  174 LEU cc_start: 0.8563 (mm) cc_final: 0.8235 (mp)
REVERT: C  188 GLU cc_start: 0.8974 (pp20) cc_final: 0.8678 (pp20)
REVERT: D   68 MET cc_start: 0.8659 (mpp) cc_final: 0.8364 (tmm)
REVERT: D  139 ARG cc_start: 0.7405 (ppt170) cc_final: 0.6828 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1581
  time to fit residues: 33.0778
Evaluate side-chains
  125 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 28 optimal weight:   20.0000
   chunk 48 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 42 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.072859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.057820 restraints weight = 28238.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.059184 restraints weight = 22376.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.060257 restraints weight = 18594.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.7234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4896  Z= 0.243
  Angle     :  0.767  11.190   6629  Z= 0.385
  Chirality :  0.045   0.165    756
  Planarity :  0.004   0.045    821
  Dihedral  :  6.268  55.823    731
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.18 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.35), residues: 579
  helix:  1.42 (0.35), residues: 222
  sheet: -0.43 (0.48), residues: 124
  loop : -2.28 (0.37), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  80 
 HIS   0.012   0.002   HIS D  71 
 PHE   0.014   0.002   PHE A  84 
 TYR   0.032   0.002   TYR A  32 
 ARG   0.004   0.001   ARG A 109 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.538 
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   32 TYR cc_start: 0.7909 (m-80) cc_final: 0.7458 (m-80)
REVERT: A   69 MET cc_start: 0.9436 (mmm) cc_final: 0.9226 (mmm)
REVERT: A  112 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8692 (mmmt)
REVERT: A  121 ILE cc_start: 0.7330 (mm) cc_final: 0.7010 (mm)
REVERT: A  128 ASP cc_start: 0.8887 (t0) cc_final: 0.8588 (t0)
REVERT: A  146 GLU cc_start: 0.6385 (tt0) cc_final: 0.5685 (tt0)
REVERT: B   47 MET cc_start: 0.7793 (tmm) cc_final: 0.7401 (tmm)
REVERT: B  122 ASP cc_start: 0.8778 (p0) cc_final: 0.8542 (p0)
REVERT: B  128 PHE cc_start: 0.8883 (p90) cc_final: 0.8588 (p90)
REVERT: B  130 PHE cc_start: 0.8341 (p90) cc_final: 0.8071 (p90)
REVERT: C  102 ASP cc_start: 0.8537 (m-30) cc_final: 0.8223 (m-30)
REVERT: C  166 PHE cc_start: 0.6927 (m-10) cc_final: 0.6137 (m-10)
REVERT: C  174 LEU cc_start: 0.8622 (mm) cc_final: 0.8265 (mp)
REVERT: C  188 GLU cc_start: 0.8995 (pp20) cc_final: 0.8694 (pp20)
REVERT: D   68 MET cc_start: 0.8582 (mpp) cc_final: 0.8319 (tmm)
REVERT: D   71 HIS cc_start: 0.7225 (m-70) cc_final: 0.6982 (m170)
REVERT: D  129 LEU cc_start: 0.9043 (mt) cc_final: 0.8792 (mt)
REVERT: D  139 ARG cc_start: 0.7461 (ppt170) cc_final: 0.6999 (ptt180)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.1658
  time to fit residues: 34.6738
Evaluate side-chains
  123 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    0.4980
   chunk 3 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0980
   chunk 50 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  26 ASN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.072846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.058088 restraints weight = 28636.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.059420 restraints weight = 22633.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.060487 restraints weight = 18853.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.7447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4896  Z= 0.223
  Angle     :  0.762  11.988   6629  Z= 0.382
  Chirality :  0.045   0.165    756
  Planarity :  0.004   0.045    821
  Dihedral  :  6.178  56.108    731
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.35), residues: 579
  helix:  1.43 (0.35), residues: 222
  sheet: -0.32 (0.48), residues: 124
  loop : -2.36 (0.37), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 148 
 HIS   0.011   0.002   HIS D  71 
 PHE   0.012   0.002   PHE A  37 
 TYR   0.025   0.002   TYR A  32 
 ARG   0.005   0.000   ARG A 109 

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 TYR cc_start: 0.7977 (m-80) cc_final: 0.7710 (m-80)
REVERT: A   69 MET cc_start: 0.9423 (mmm) cc_final: 0.9189 (mmm)
REVERT: A  112 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8702 (mmmt)
REVERT: A  121 ILE cc_start: 0.7321 (mm) cc_final: 0.7010 (mm)
REVERT: A  128 ASP cc_start: 0.8880 (t0) cc_final: 0.8585 (t0)
REVERT: A  146 GLU cc_start: 0.6385 (tt0) cc_final: 0.5636 (tt0)
REVERT: B   47 MET cc_start: 0.7912 (tmm) cc_final: 0.7548 (tmm)
REVERT: B  122 ASP cc_start: 0.8706 (p0) cc_final: 0.8459 (p0)
REVERT: C  102 ASP cc_start: 0.8511 (m-30) cc_final: 0.8187 (m-30)
REVERT: C  166 PHE cc_start: 0.6948 (m-10) cc_final: 0.6282 (m-10)
REVERT: C  174 LEU cc_start: 0.8645 (mm) cc_final: 0.8262 (mp)
REVERT: C  188 GLU cc_start: 0.8999 (pp20) cc_final: 0.8702 (pp20)
REVERT: D   68 MET cc_start: 0.8595 (mpp) cc_final: 0.8362 (tmm)
REVERT: D   71 HIS cc_start: 0.7169 (m-70) cc_final: 0.6909 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1641
  time to fit residues: 32.8010
Evaluate side-chains
  122 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.073543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.058646 restraints weight = 28652.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.060053 restraints weight = 22535.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.061108 restraints weight = 18632.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.7477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4896  Z= 0.201
  Angle     :  0.749  10.826   6629  Z= 0.373
  Chirality :  0.045   0.162    756
  Planarity :  0.004   0.043    821
  Dihedral  :  6.116  56.178    731
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.35), residues: 579
  helix:  1.42 (0.35), residues: 222
  sheet: -0.29 (0.48), residues: 124
  loop : -2.35 (0.37), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 148 
 HIS   0.011   0.001   HIS D  71 
 PHE   0.012   0.002   PHE A  37 
 TYR   0.027   0.002   TYR A  32 
 ARG   0.002   0.000   ARG A 109 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1774.79 seconds
wall clock time: 32 minutes 31.04 seconds (1951.04 seconds total)