Starting phenix.real_space_refine
on Mon Feb 10 21:04:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mlu_9146/02_2025/6mlu_9146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mlu_9146/02_2025/6mlu_9146.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mlu_9146/02_2025/6mlu_9146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mlu_9146/02_2025/6mlu_9146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mlu_9146/02_2025/6mlu_9146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mlu_9146/02_2025/6mlu_9146.cif"
  }
  resolution = 4.0
  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=   0.007
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      28      5.16       5
     C    1616      2.51       5
     N     426      2.21       5
     O     446      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2516
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1258
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 9, 'TRANS': 143}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.50, per 1000 atoms: 0.99
  Number of scatterers: 2516
  At special positions: 0
  Unit cell: (72.05, 73.36, 58.95, 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      28     16.00
     O     446      8.00
     N     426      7.00
     C    1616      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 149 " - pdb=" SG  CYS A 164 " distance=2.04

  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: 0.67
  Conformation dependent library (CDL) restraints added in 316.8 milliseconds
  

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  596

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 6 sheets defined
      24.2% alpha, 37.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 114 through 125
    Processing helix  chain 'A' and resid 137 through 142
    Processing helix  chain 'A' and resid 173 through 184
    Processing helix  chain 'A' and resid 184 through 190
    Processing helix  chain 'B' and resid 114 through 125
    Processing helix  chain 'B' and resid 137 through 142
    Processing helix  chain 'B' and resid 173 through 184
    Processing helix  chain 'B' and resid 184 through 190
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 93
      removed outlier: 4.585A  pdb=" N   VAL A 232 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR A 231 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 167
      removed outlier: 7.097A  pdb=" N   LEU A 159 " --> pdb=" O   ASP A 154 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ASP A 154 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 161 " --> pdb=" O   MET A 152 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   ARG A 153 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 167
      removed outlier: 7.097A  pdb=" N   LEU A 159 " --> pdb=" O   ASP A 154 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ASP A 154 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 161 " --> pdb=" O   MET A 152 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 93
      removed outlier: 4.583A  pdb=" N   VAL B 232 " --> pdb=" O   GLN B  93 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR B 231 " --> pdb=" O   ASP B 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 167
      removed outlier: 7.097A  pdb=" N   LEU B 159 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ASP B 154 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY B 161 " --> pdb=" O   MET B 152 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   ARG B 153 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 167
      removed outlier: 7.097A  pdb=" N   LEU B 159 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ASP B 154 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY B 161 " --> pdb=" O   MET B 152 " (cutoff:3.500A)

    108 hydrogen bonds defined for protein.
    300 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: 0.60

  Time building geometry restraints manager: 0.71 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: 796
        1.34 -     1.46: 577
        1.46 -     1.58: 1159
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 2580
  Sorted by residual:
  bond pdb=" CA  HIS A 110 "
       pdb=" CB  HIS A 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.564 -0.033 1.69e-02 3.50e+03 3.91e+00
  bond pdb=" CA  HIS B 110 "
       pdb=" CB  HIS B 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.564 -0.033 1.69e-02 3.50e+03 3.89e+00
  bond pdb=" CA  ARG A  88 "
       pdb=" C   ARG A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.555 -0.030 2.10e-02 2.27e+03 2.02e+00
  bond pdb=" CA  ARG B  88 "
       pdb=" C   ARG B  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.554 -0.029 2.10e-02 2.27e+03 1.88e+00
  bond pdb=" N   HIS B 110 "
       pdb=" CA  HIS B 110 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.45e+00
  ... (remaining 2575 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 3337
        2.09 -     4.17: 117
        4.17 -     6.26: 25
        6.26 -     8.34: 9
        8.34 -    10.43: 6
  Bond angle restraints: 3494
  Sorted by residual:
  angle pdb=" C   ALA A 109 "
        pdb=" N   HIS A 110 "
        pdb=" CA  HIS A 110 "
      ideal   model   delta    sigma   weight residual
     121.54  131.86  -10.32 1.91e+00 2.74e-01 2.92e+01
  angle pdb=" C   ALA B 109 "
        pdb=" N   HIS B 110 "
        pdb=" CA  HIS B 110 "
      ideal   model   delta    sigma   weight residual
     121.54  131.66  -10.12 1.91e+00 2.74e-01 2.81e+01
  angle pdb=" C   LEU B  98 "
        pdb=" N   GLU B  99 "
        pdb=" CA  GLU B  99 "
      ideal   model   delta    sigma   weight residual
     121.54  130.14   -8.60 1.91e+00 2.74e-01 2.03e+01
  angle pdb=" C   LEU A  98 "
        pdb=" N   GLU A  99 "
        pdb=" CA  GLU A  99 "
      ideal   model   delta    sigma   weight residual
     121.54  130.01   -8.47 1.91e+00 2.74e-01 1.96e+01
  angle pdb=" C   LEU B 208 "
        pdb=" N   GLU B 209 "
        pdb=" CA  GLU B 209 "
      ideal   model   delta    sigma   weight residual
     121.54  128.30   -6.76 1.91e+00 2.74e-01 1.25e+01
  ... (remaining 3489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.37: 1401
       11.37 -    22.73: 134
       22.73 -    34.09: 24
       34.09 -    45.46: 12
       45.46 -    56.82: 4
  Dihedral angle restraints: 1575
    sinusoidal: 661
      harmonic: 914
  Sorted by residual:
  dihedral pdb=" CA  HIS B 110 "
           pdb=" C   HIS B 110 "
           pdb=" N   VAL B 111 "
           pdb=" CA  VAL B 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.73   23.27     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  HIS A 110 "
           pdb=" C   HIS A 110 "
           pdb=" N   VAL A 111 "
           pdb=" CA  VAL A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.82   23.18     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  TRP A 192 "
           pdb=" C   TRP A 192 "
           pdb=" N   LYS A 193 "
           pdb=" CA  LYS A 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.35   22.65     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 1572 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 277
       0.055 -    0.109: 74
       0.109 -    0.164: 28
       0.164 -    0.218: 7
       0.218 -    0.273: 2
  Chirality restraints: 388
  Sorted by residual:
  chirality pdb=" CA  HIS B 110 "
            pdb=" N   HIS B 110 "
            pdb=" C   HIS B 110 "
            pdb=" CB  HIS B 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  HIS A 110 "
            pdb=" N   HIS A 110 "
            pdb=" C   HIS A 110 "
            pdb=" CB  HIS A 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CB  THR B 100 "
            pdb=" CA  THR B 100 "
            pdb=" OG1 THR B 100 "
            pdb=" CG2 THR B 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 385 not shown)

  Planarity restraints: 440
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 209 "    0.012 2.00e-02 2.50e+03   2.44e-02 5.95e+00
        pdb=" C   GLU B 209 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   GLU B 209 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU B 210 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 209 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.91e+00
        pdb=" C   GLU A 209 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   GLU A 209 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU A 210 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 109 "    0.009 2.00e-02 2.50e+03   1.80e-02 3.24e+00
        pdb=" C   ALA B 109 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   ALA B 109 "    0.012 2.00e-02 2.50e+03
        pdb=" N   HIS B 110 "    0.010 2.00e-02 2.50e+03
  ... (remaining 437 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 20
        2.61 -     3.18: 2019
        3.18 -     3.76: 3936
        3.76 -     4.33: 5183
        4.33 -     4.90: 8446
  Nonbonded interactions: 19604
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 149 "
            pdb=" SG  CYS B 164 "
     model   vdw
     2.040 3.760
  nonbonded pdb=" OD1 ASP A 154 "
            pdb=" N   MET A 158 "
     model   vdw
     2.406 3.120
  nonbonded pdb=" OD1 ASP B 154 "
            pdb=" N   MET B 158 "
     model   vdw
     2.409 3.120
  nonbonded pdb=" NH1 ARG B 206 "
            pdb=" O   PHE B 240 "
     model   vdw
     2.415 3.120
  nonbonded pdb=" NH1 ARG A 206 "
            pdb=" O   PHE A 240 "
     model   vdw
     2.415 3.120
  ... (remaining 19599 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.690
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.450
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
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      :  0.005   0.044   2580  Z= 0.344
  Angle     :  1.046  10.429   3494  Z= 0.564
  Chirality :  0.064   0.273    388
  Planarity :  0.007   0.036    440
  Dihedral  :  9.856  47.411    976
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  2.78 %
    Favored  : 96.53 %
  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: -4.38 (0.42), residues: 302
  helix: -2.79 (0.45), residues: 74
  sheet: -1.76 (0.57), residues: 86
  loop : -3.75 (0.42), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 192 
 HIS   0.013   0.004   HIS A 110 
 PHE   0.015   0.003   PHE A 196 
 TYR   0.008   0.002   TYR B 155 
 ARG   0.002   0.000   ARG A 177 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.8839 (m-30) cc_final: 0.8375 (m-30)
REVERT: A  137 SER cc_start: 0.9203 (t) cc_final: 0.8998 (p)
REVERT: A  147 MET cc_start: 0.8306 (mmm) cc_final: 0.7641 (tpp)
REVERT: A  165 ARG cc_start: 0.7552 (mmt-90) cc_final: 0.7122 (mmt180)
REVERT: A  177 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7831 (mtm-85)
REVERT: A  195 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7635 (mt-10)
REVERT: A  197 GLN cc_start: 0.8825 (mt0) cc_final: 0.8597 (mp-120)
REVERT: A  198 GLN cc_start: 0.8748 (mt0) cc_final: 0.8529 (mt0)
REVERT: A  202 GLU cc_start: 0.8764 (tt0) cc_final: 0.8201 (tm-30)
REVERT: A  204 PHE cc_start: 0.8056 (m-80) cc_final: 0.7746 (m-80)
REVERT: A  223 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8401 (mm-40)
REVERT: A  232 VAL cc_start: 0.9659 (t) cc_final: 0.8480 (t)
REVERT: A  236 ILE cc_start: 0.9238 (mt) cc_final: 0.8963 (tp)
REVERT: A  237 VAL cc_start: 0.8740 (m) cc_final: 0.8274 (p)
REVERT: A  239 ASP cc_start: 0.8777 (m-30) cc_final: 0.8247 (m-30)
REVERT: B  115 LYS cc_start: 0.6956 (ttmp) cc_final: 0.6727 (tptm)
REVERT: B  133 ASP cc_start: 0.8724 (m-30) cc_final: 0.8410 (m-30)
REVERT: B  177 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.8038 (mtm-85)
REVERT: B  202 GLU cc_start: 0.8888 (tt0) cc_final: 0.8301 (tm-30)
REVERT: B  232 VAL cc_start: 0.9717 (t) cc_final: 0.8700 (t)
REVERT: B  236 ILE cc_start: 0.9343 (mt) cc_final: 0.9043 (tp)
REVERT: B  237 VAL cc_start: 0.8879 (m) cc_final: 0.8238 (p)
REVERT: B  239 ASP cc_start: 0.8877 (m-30) cc_final: 0.8536 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2252
  time to fit residues: 40.4547
Evaluate side-chains
  124 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 118 GLN
A 213 HIS
B 139 GLN
B 162 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.111987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.089807 restraints weight = 7201.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.092620 restraints weight = 4091.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.094502 restraints weight = 2851.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.4282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2580  Z= 0.229
  Angle     :  0.811   7.547   3494  Z= 0.424
  Chirality :  0.054   0.203    388
  Planarity :  0.006   0.031    440
  Dihedral  :  6.272  23.428    336
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 16.67 %
    Favored  : 76.39 %
  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: -3.27 (0.46), residues: 302
  helix: -0.63 (0.58), residues: 74
  sheet: -1.75 (0.53), residues: 90
  loop : -3.38 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 192 
 HIS   0.010   0.002   HIS B 110 
 PHE   0.017   0.001   PHE B 106 
 TYR   0.009   0.001   TYR A 219 
 ARG   0.004   0.001   ARG A  88 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8718 (pm20) cc_final: 0.8435 (pm20)
REVERT: A   95 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7954 (tppt)
REVERT: A   99 GLU cc_start: 0.8157 (pm20) cc_final: 0.7639 (pm20)
REVERT: A  120 LEU cc_start: 0.8661 (mt) cc_final: 0.8300 (mt)
REVERT: A  124 GLN cc_start: 0.7124 (mp10) cc_final: 0.5796 (tm-30)
REVERT: A  133 ASP cc_start: 0.8682 (m-30) cc_final: 0.8172 (m-30)
REVERT: A  147 MET cc_start: 0.8222 (mmm) cc_final: 0.7606 (tpp)
REVERT: A  165 ARG cc_start: 0.8292 (mmt-90) cc_final: 0.7310 (mmt180)
REVERT: A  198 GLN cc_start: 0.8589 (mt0) cc_final: 0.8303 (mt0)
REVERT: A  202 GLU cc_start: 0.8442 (tt0) cc_final: 0.7933 (tm-30)
REVERT: A  204 PHE cc_start: 0.8113 (m-80) cc_final: 0.7428 (m-80)
REVERT: A  213 HIS cc_start: 0.7637 (m90) cc_final: 0.7382 (m-70)
REVERT: A  230 TYR cc_start: 0.9152 (m-80) cc_final: 0.8678 (m-80)
REVERT: A  236 ILE cc_start: 0.9253 (mt) cc_final: 0.9032 (tp)
REVERT: A  237 VAL cc_start: 0.9081 (m) cc_final: 0.8546 (p)
REVERT: A  239 ASP cc_start: 0.8753 (m-30) cc_final: 0.8274 (m-30)
REVERT: B  115 LYS cc_start: 0.6875 (ttmp) cc_final: 0.6530 (tptm)
REVERT: B  120 LEU cc_start: 0.8832 (mt) cc_final: 0.8361 (mm)
REVERT: B  121 MET cc_start: 0.7150 (tmm) cc_final: 0.6891 (tpp)
REVERT: B  127 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8079 (ptmt)
REVERT: B  133 ASP cc_start: 0.8519 (m-30) cc_final: 0.8291 (m-30)
REVERT: B  152 MET cc_start: 0.7460 (mmm) cc_final: 0.7065 (mmm)
REVERT: B  202 GLU cc_start: 0.8792 (tt0) cc_final: 0.8440 (tm-30)
REVERT: B  204 PHE cc_start: 0.8186 (m-80) cc_final: 0.7825 (m-10)
REVERT: B  211 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.7981 (mmp80)
REVERT: B  236 ILE cc_start: 0.9342 (mt) cc_final: 0.8995 (tp)
REVERT: B  237 VAL cc_start: 0.9062 (m) cc_final: 0.8169 (p)
REVERT: B  239 ASP cc_start: 0.8878 (m-30) cc_final: 0.8074 (p0)
  outliers start: 20
  outliers final: 10
  residues processed: 140
  average time/residue: 0.1925
  time to fit residues: 30.1559
Evaluate side-chains
  133 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  227 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 7 optimal weight:    9.9990
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    7.9990
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 140 ASN
A 197 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.109551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.087924 restraints weight = 7248.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.090545 restraints weight = 4149.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.092362 restraints weight = 2894.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.5367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2580  Z= 0.262
  Angle     :  0.785   7.529   3494  Z= 0.410
  Chirality :  0.053   0.218    388
  Planarity :  0.005   0.027    440
  Dihedral  :  6.177  22.423    336
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 21.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  9.38 %
    Allowed  : 21.53 %
    Favored  : 69.10 %
  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: -2.95 (0.46), residues: 302
  helix:  0.12 (0.59), residues: 74
  sheet: -2.07 (0.51), residues: 94
  loop : -3.09 (0.50), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 182 
 HIS   0.013   0.003   HIS A 110 
 PHE   0.018   0.002   PHE B 106 
 TYR   0.027   0.002   TYR B 126 
 ARG   0.003   0.000   ARG A  88 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7772 (tptm) cc_final: 0.7338 (mttm)
REVERT: A  119 LEU cc_start: 0.7820 (mt) cc_final: 0.7570 (mt)
REVERT: A  120 LEU cc_start: 0.8699 (mt) cc_final: 0.8254 (mt)
REVERT: A  124 GLN cc_start: 0.8025 (mp10) cc_final: 0.7284 (tm-30)
REVERT: A  133 ASP cc_start: 0.8699 (m-30) cc_final: 0.8085 (m-30)
REVERT: A  136 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8317 (mp0)
REVERT: A  152 MET cc_start: 0.7161 (mmm) cc_final: 0.6799 (mmm)
REVERT: A  198 GLN cc_start: 0.8537 (mt0) cc_final: 0.8089 (mt0)
REVERT: A  204 PHE cc_start: 0.8067 (m-80) cc_final: 0.7709 (m-80)
REVERT: A  213 HIS cc_start: 0.7781 (m90) cc_final: 0.7521 (m-70)
REVERT: A  223 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8226 (mm-40)
REVERT: A  230 TYR cc_start: 0.9154 (m-80) cc_final: 0.8619 (m-80)
REVERT: A  236 ILE cc_start: 0.9355 (mt) cc_final: 0.8926 (tp)
REVERT: A  237 VAL cc_start: 0.9115 (m) cc_final: 0.8515 (p)
REVERT: A  239 ASP cc_start: 0.8805 (m-30) cc_final: 0.8287 (m-30)
REVERT: B  115 LYS cc_start: 0.7158 (ttmp) cc_final: 0.6702 (tptp)
REVERT: B  120 LEU cc_start: 0.8740 (mt) cc_final: 0.8510 (mm)
REVERT: B  121 MET cc_start: 0.7099 (tmm) cc_final: 0.6888 (tpp)
REVERT: B  124 GLN cc_start: 0.8197 (mp10) cc_final: 0.7927 (tm-30)
REVERT: B  126 TYR cc_start: 0.7424 (m-80) cc_final: 0.7082 (m-80)
REVERT: B  127 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8205 (ptmt)
REVERT: B  136 GLU cc_start: 0.8694 (mp0) cc_final: 0.8423 (mp0)
REVERT: B  152 MET cc_start: 0.7627 (mmm) cc_final: 0.7053 (mmm)
REVERT: B  195 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7283 (mt-10)
REVERT: B  204 PHE cc_start: 0.8516 (m-80) cc_final: 0.7923 (m-10)
REVERT: B  215 ILE cc_start: 0.7967 (mm) cc_final: 0.7387 (mm)
REVERT: B  218 VAL cc_start: 0.9381 (m) cc_final: 0.9156 (t)
REVERT: B  236 ILE cc_start: 0.9338 (mt) cc_final: 0.9031 (tp)
REVERT: B  237 VAL cc_start: 0.9108 (m) cc_final: 0.8257 (p)
REVERT: B  239 ASP cc_start: 0.8862 (m-30) cc_final: 0.7988 (p0)
  outliers start: 27
  outliers final: 18
  residues processed: 132
  average time/residue: 0.1974
  time to fit residues: 29.2316
Evaluate side-chains
  132 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 14 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    2.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN
** B 198 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 = 0.3697 r_free = 0.3697 target = 0.110725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.089453 restraints weight = 7194.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.092082 restraints weight = 4043.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.093854 restraints weight = 2799.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.5877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2580  Z= 0.249
  Angle     :  0.762   7.235   3494  Z= 0.398
  Chirality :  0.052   0.216    388
  Planarity :  0.005   0.035    440
  Dihedral  :  6.038  22.585    336
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 20.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  9.03 %
    Allowed  : 20.83 %
    Favored  : 70.14 %
  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: -2.65 (0.47), residues: 302
  helix:  0.57 (0.60), residues: 74
  sheet: -1.93 (0.52), residues: 94
  loop : -3.00 (0.50), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 192 
 HIS   0.011   0.003   HIS A 110 
 PHE   0.022   0.002   PHE B 106 
 TYR   0.036   0.002   TYR A 126 
 ARG   0.003   0.000   ARG B 211 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8165 (tppt)
REVERT: A  115 LYS cc_start: 0.7542 (tptm) cc_final: 0.7251 (mttm)
REVERT: A  133 ASP cc_start: 0.8664 (m-30) cc_final: 0.7941 (m-30)
REVERT: A  136 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8309 (mp0)
REVERT: A  139 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7835 (tp-100)
REVERT: A  152 MET cc_start: 0.7258 (mmm) cc_final: 0.6992 (mmm)
REVERT: A  198 GLN cc_start: 0.8518 (mt0) cc_final: 0.7885 (mt0)
REVERT: A  213 HIS cc_start: 0.7613 (m90) cc_final: 0.7360 (m-70)
REVERT: A  230 TYR cc_start: 0.9184 (m-80) cc_final: 0.8724 (m-80)
REVERT: A  236 ILE cc_start: 0.9366 (mt) cc_final: 0.8872 (tp)
REVERT: A  237 VAL cc_start: 0.9112 (m) cc_final: 0.8617 (p)
REVERT: A  239 ASP cc_start: 0.8706 (m-30) cc_final: 0.8150 (m-30)
REVERT: B  115 LYS cc_start: 0.7466 (ttmp) cc_final: 0.6830 (tptp)
REVERT: B  116 LYS cc_start: 0.7117 (pmtt) cc_final: 0.6553 (ptmm)
REVERT: B  124 GLN cc_start: 0.8223 (mp10) cc_final: 0.7915 (tm-30)
REVERT: B  126 TYR cc_start: 0.7164 (m-80) cc_final: 0.6939 (m-80)
REVERT: B  127 LYS cc_start: 0.8893 (ptmt) cc_final: 0.8692 (ptmt)
REVERT: B  136 GLU cc_start: 0.8688 (mp0) cc_final: 0.8196 (mp0)
REVERT: B  195 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7270 (tt0)
REVERT: B  223 GLN cc_start: 0.8413 (mm110) cc_final: 0.8167 (mm-40)
REVERT: B  236 ILE cc_start: 0.9301 (mt) cc_final: 0.9003 (tp)
REVERT: B  237 VAL cc_start: 0.9061 (m) cc_final: 0.8555 (p)
REVERT: B  239 ASP cc_start: 0.8871 (m-30) cc_final: 0.8454 (m-30)
  outliers start: 26
  outliers final: 18
  residues processed: 129
  average time/residue: 0.2063
  time to fit residues: 29.9415
Evaluate side-chains
  132 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN
** B 198 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 = 0.3681 r_free = 0.3681 target = 0.110175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.088992 restraints weight = 7299.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.091721 restraints weight = 4022.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.093516 restraints weight = 2759.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.6127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   2580  Z= 0.261
  Angle     :  0.795   7.187   3494  Z= 0.412
  Chirality :  0.054   0.209    388
  Planarity :  0.005   0.031    440
  Dihedral  :  6.070  22.163    336
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 21.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers : 11.46 %
    Allowed  : 22.57 %
    Favored  : 65.97 %
  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: -2.42 (0.48), residues: 302
  helix:  0.87 (0.60), residues: 72
  sheet: -1.76 (0.53), residues: 94
  loop : -2.90 (0.50), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 192 
 HIS   0.012   0.003   HIS B 110 
 PHE   0.019   0.002   PHE B 106 
 TYR   0.026   0.002   TYR A 126 
 ARG   0.003   0.000   ARG B 211 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8918 (pp30) cc_final: 0.8428 (pm20)
REVERT: A   95 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7857 (tppt)
REVERT: A  133 ASP cc_start: 0.8609 (m-30) cc_final: 0.7867 (m-30)
REVERT: A  136 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7299 (mp0)
REVERT: A  139 GLN cc_start: 0.8290 (tp-100) cc_final: 0.7904 (tp-100)
REVERT: A  198 GLN cc_start: 0.8391 (mt0) cc_final: 0.7754 (mt0)
REVERT: A  213 HIS cc_start: 0.7504 (m90) cc_final: 0.7210 (m-70)
REVERT: A  221 GLU cc_start: 0.7303 (tm-30) cc_final: 0.7010 (pp20)
REVERT: A  230 TYR cc_start: 0.9169 (m-80) cc_final: 0.8831 (m-80)
REVERT: A  236 ILE cc_start: 0.9345 (mt) cc_final: 0.8640 (tp)
REVERT: A  237 VAL cc_start: 0.9107 (m) cc_final: 0.8645 (p)
REVERT: A  239 ASP cc_start: 0.8788 (m-30) cc_final: 0.8313 (m-30)
REVERT: B  115 LYS cc_start: 0.7570 (ttmp) cc_final: 0.6829 (tptp)
REVERT: B  116 LYS cc_start: 0.7071 (pmtt) cc_final: 0.6566 (ptmm)
REVERT: B  120 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8271 (mm)
REVERT: B  124 GLN cc_start: 0.8217 (mp10) cc_final: 0.7877 (tm-30)
REVERT: B  127 LYS cc_start: 0.8822 (ptmt) cc_final: 0.8056 (ptmt)
REVERT: B  136 GLU cc_start: 0.8723 (mp0) cc_final: 0.8310 (mp0)
REVERT: B  204 PHE cc_start: 0.8266 (m-80) cc_final: 0.7771 (m-10)
REVERT: B  223 GLN cc_start: 0.8426 (mm110) cc_final: 0.8180 (mm-40)
REVERT: B  236 ILE cc_start: 0.9375 (mt) cc_final: 0.8983 (tp)
REVERT: B  237 VAL cc_start: 0.9053 (m) cc_final: 0.8061 (p)
REVERT: B  239 ASP cc_start: 0.8865 (m-30) cc_final: 0.7853 (p0)
  outliers start: 33
  outliers final: 23
  residues processed: 129
  average time/residue: 0.2080
  time to fit residues: 30.1137
Evaluate side-chains
  136 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue   99 GLU
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 18 optimal weight:   20.0000
   chunk 8 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   chunk 7 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 GLN
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 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 = 0.3730 r_free = 0.3730 target = 0.113482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.091831 restraints weight = 7313.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.094541 restraints weight = 4195.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.096225 restraints weight = 2923.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.6518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2580  Z= 0.210
  Angle     :  0.799   7.165   3494  Z= 0.412
  Chirality :  0.053   0.200    388
  Planarity :  0.005   0.036    440
  Dihedral  :  6.045  22.956    336
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 20.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  8.68 %
    Allowed  : 25.00 %
    Favored  : 66.32 %
  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: -2.38 (0.49), residues: 302
  helix:  0.82 (0.64), residues: 72
  sheet: -1.41 (0.54), residues: 90
  loop : -3.08 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 182 
 HIS   0.013   0.002   HIS B 110 
 PHE   0.016   0.002   PHE B 106 
 TYR   0.026   0.002   TYR B 126 
 ARG   0.003   0.001   ARG A 177 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7611 (tppt)
REVERT: A  133 ASP cc_start: 0.8575 (m-30) cc_final: 0.8003 (m-30)
REVERT: A  198 GLN cc_start: 0.8306 (mt0) cc_final: 0.7905 (mt0)
REVERT: A  202 GLU cc_start: 0.7973 (tp30) cc_final: 0.7638 (tp30)
REVERT: A  221 GLU cc_start: 0.7133 (tm-30) cc_final: 0.5970 (pp20)
REVERT: A  223 GLN cc_start: 0.8818 (mm-40) cc_final: 0.7997 (mm-40)
REVERT: A  230 TYR cc_start: 0.9072 (m-80) cc_final: 0.8546 (m-80)
REVERT: A  236 ILE cc_start: 0.9204 (mt) cc_final: 0.8730 (tp)
REVERT: A  237 VAL cc_start: 0.8993 (m) cc_final: 0.8170 (p)
REVERT: A  239 ASP cc_start: 0.8654 (m-30) cc_final: 0.8235 (m-30)
REVERT: B  116 LYS cc_start: 0.7115 (pmtt) cc_final: 0.6687 (ptmm)
REVERT: B  124 GLN cc_start: 0.8210 (mp10) cc_final: 0.7949 (tm-30)
REVERT: B  126 TYR cc_start: 0.6668 (m-80) cc_final: 0.6065 (m-80)
REVERT: B  127 LYS cc_start: 0.8595 (ptmt) cc_final: 0.8347 (ptmt)
REVERT: B  135 PRO cc_start: 0.9507 (Cg_endo) cc_final: 0.9129 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8654 (mp0) cc_final: 0.8260 (mp0)
REVERT: B  195 GLU cc_start: 0.7186 (tt0) cc_final: 0.6591 (tt0)
REVERT: B  202 GLU cc_start: 0.8046 (tp30) cc_final: 0.7408 (tp30)
REVERT: B  204 PHE cc_start: 0.8182 (m-80) cc_final: 0.7898 (m-10)
REVERT: B  215 ILE cc_start: 0.7916 (mm) cc_final: 0.7452 (mm)
REVERT: B  223 GLN cc_start: 0.8291 (mm110) cc_final: 0.8057 (mm-40)
REVERT: B  226 LYS cc_start: 0.9287 (mmmm) cc_final: 0.9051 (mmmt)
REVERT: B  236 ILE cc_start: 0.9238 (mt) cc_final: 0.8863 (tp)
REVERT: B  237 VAL cc_start: 0.9023 (m) cc_final: 0.8219 (p)
REVERT: B  239 ASP cc_start: 0.8803 (m-30) cc_final: 0.8349 (m-30)
  outliers start: 25
  outliers final: 16
  residues processed: 128
  average time/residue: 0.2003
  time to fit residues: 28.7722
Evaluate side-chains
  139 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue   99 GLU
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   chunk 28 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0870
   chunk 14 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.8166

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 GLN
A 213 HIS
A 235 HIS
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.111479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.090063 restraints weight = 7475.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.092839 restraints weight = 4167.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.094638 restraints weight = 2875.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.6781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   2580  Z= 0.264
  Angle     :  0.841   7.508   3494  Z= 0.431
  Chirality :  0.053   0.211    388
  Planarity :  0.005   0.032    440
  Dihedral  :  6.075  23.293    336
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 24.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 24.65 %
    Favored  : 67.01 %
  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: -2.38 (0.49), residues: 302
  helix:  1.04 (0.63), residues: 72
  sheet: -1.44 (0.57), residues: 82
  loop : -3.12 (0.48), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 192 
 HIS   0.013   0.003   HIS B 110 
 PHE   0.015   0.002   PHE B 106 
 TYR   0.021   0.002   TYR B 126 
 ARG   0.006   0.001   ARG B 211 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7843 (tppt)
REVERT: A  133 ASP cc_start: 0.8599 (m-30) cc_final: 0.7974 (m-30)
REVERT: A  198 GLN cc_start: 0.8248 (mt0) cc_final: 0.7774 (mt0)
REVERT: A  211 ARG cc_start: 0.8471 (mmm-85) cc_final: 0.8212 (mmp80)
REVERT: A  221 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6324 (pp20)
REVERT: A  223 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8161 (mm-40)
REVERT: A  230 TYR cc_start: 0.9148 (m-80) cc_final: 0.8655 (m-80)
REVERT: A  236 ILE cc_start: 0.9247 (mt) cc_final: 0.8733 (tp)
REVERT: A  237 VAL cc_start: 0.9073 (m) cc_final: 0.8277 (p)
REVERT: A  239 ASP cc_start: 0.8536 (m-30) cc_final: 0.7998 (m-30)
REVERT: B  116 LYS cc_start: 0.7150 (pmtt) cc_final: 0.6756 (ptmm)
REVERT: B  120 LEU cc_start: 0.8959 (mm) cc_final: 0.8754 (mp)
REVERT: B  127 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8404 (ptmt)
REVERT: B  135 PRO cc_start: 0.9513 (Cg_endo) cc_final: 0.9116 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8652 (mp0) cc_final: 0.8319 (mp0)
REVERT: B  195 GLU cc_start: 0.7315 (tt0) cc_final: 0.6750 (tt0)
REVERT: B  202 GLU cc_start: 0.8025 (tp30) cc_final: 0.7452 (tp30)
REVERT: B  204 PHE cc_start: 0.8223 (m-80) cc_final: 0.7960 (m-10)
REVERT: B  211 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8009 (mmm-85)
REVERT: B  226 LYS cc_start: 0.9347 (mmmm) cc_final: 0.8981 (mmmt)
REVERT: B  236 ILE cc_start: 0.9274 (mt) cc_final: 0.8830 (tp)
REVERT: B  237 VAL cc_start: 0.8989 (m) cc_final: 0.8173 (p)
REVERT: B  239 ASP cc_start: 0.8781 (m-30) cc_final: 0.8254 (m-30)
  outliers start: 24
  outliers final: 17
  residues processed: 132
  average time/residue: 0.2119
  time to fit residues: 31.2382
Evaluate side-chains
  134 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue   99 GLU
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 235 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.110105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.088729 restraints weight = 7468.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.091523 restraints weight = 4198.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.093282 restraints weight = 2911.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.6970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   2580  Z= 0.305
  Angle     :  0.895  10.506   3494  Z= 0.457
  Chirality :  0.055   0.204    388
  Planarity :  0.005   0.030    440
  Dihedral  :  6.277  22.681    336
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 27.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.58 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 24.65 %
    Favored  : 67.01 %
  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: -2.37 (0.49), residues: 302
  helix:  0.85 (0.63), residues: 72
  sheet: -1.49 (0.58), residues: 82
  loop : -2.97 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 192 
 HIS   0.013   0.003   HIS B 110 
 PHE   0.020   0.002   PHE B 106 
 TYR   0.025   0.002   TYR A 126 
 ARG   0.006   0.001   ARG B 211 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.8626 (m-30) cc_final: 0.7993 (m-30)
REVERT: A  197 GLN cc_start: 0.7931 (mp10) cc_final: 0.7626 (mp10)
REVERT: A  198 GLN cc_start: 0.8148 (mt0) cc_final: 0.7634 (mt0)
REVERT: A  221 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7221 (pp20)
REVERT: A  230 TYR cc_start: 0.9169 (m-80) cc_final: 0.8703 (m-80)
REVERT: A  236 ILE cc_start: 0.9258 (mt) cc_final: 0.8656 (tp)
REVERT: A  237 VAL cc_start: 0.9044 (m) cc_final: 0.8520 (p)
REVERT: A  239 ASP cc_start: 0.8692 (m-30) cc_final: 0.8194 (m-30)
REVERT: B  116 LYS cc_start: 0.7101 (pmtt) cc_final: 0.6572 (ptmm)
REVERT: B  120 LEU cc_start: 0.8841 (mm) cc_final: 0.8386 (mp)
REVERT: B  124 GLN cc_start: 0.7980 (mp10) cc_final: 0.7742 (tm-30)
REVERT: B  127 LYS cc_start: 0.8601 (ptmt) cc_final: 0.8392 (ptmt)
REVERT: B  135 PRO cc_start: 0.9525 (Cg_endo) cc_final: 0.9088 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8723 (mp0) cc_final: 0.8500 (mp0)
REVERT: B  195 GLU cc_start: 0.7651 (tt0) cc_final: 0.7332 (tt0)
REVERT: B  202 GLU cc_start: 0.8045 (tp30) cc_final: 0.7506 (tp30)
REVERT: B  204 PHE cc_start: 0.8227 (m-80) cc_final: 0.7891 (m-10)
REVERT: B  211 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.8030 (mmm-85)
REVERT: B  226 LYS cc_start: 0.9301 (mmmm) cc_final: 0.8942 (mmmt)
REVERT: B  236 ILE cc_start: 0.9327 (mt) cc_final: 0.8852 (tp)
REVERT: B  237 VAL cc_start: 0.8990 (m) cc_final: 0.8165 (p)
REVERT: B  239 ASP cc_start: 0.8926 (m-30) cc_final: 0.8455 (m-30)
  outliers start: 24
  outliers final: 17
  residues processed: 130
  average time/residue: 0.2134
  time to fit residues: 31.0158
Evaluate side-chains
  131 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 14 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 235 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 = 0.3708 r_free = 0.3708 target = 0.113589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.091880 restraints weight = 7264.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.094548 restraints weight = 4191.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.096263 restraints weight = 2940.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.7232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   2580  Z= 0.255
  Angle     :  0.964  14.433   3494  Z= 0.471
  Chirality :  0.056   0.208    388
  Planarity :  0.005   0.034    440
  Dihedral  :  6.272  22.793    336
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 24.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 29.17 %
    Favored  : 64.93 %
  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: -2.31 (0.49), residues: 302
  helix:  0.91 (0.62), residues: 72
  sheet: -1.45 (0.59), residues: 82
  loop : -2.94 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 182 
 HIS   0.012   0.002   HIS B 110 
 PHE   0.020   0.002   PHE B 106 
 TYR   0.035   0.002   TYR A 126 
 ARG   0.010   0.001   ARG A 177 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.8573 (m-30) cc_final: 0.7869 (m-30)
REVERT: A  197 GLN cc_start: 0.8015 (mp10) cc_final: 0.7704 (mp10)
REVERT: A  198 GLN cc_start: 0.8196 (mt0) cc_final: 0.7681 (mt0)
REVERT: A  206 ARG cc_start: 0.7826 (mmm160) cc_final: 0.7200 (mmm160)
REVERT: A  211 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8063 (mmp80)
REVERT: A  230 TYR cc_start: 0.9155 (m-80) cc_final: 0.8709 (m-80)
REVERT: A  236 ILE cc_start: 0.9204 (mt) cc_final: 0.8712 (tp)
REVERT: A  237 VAL cc_start: 0.8940 (m) cc_final: 0.8032 (p)
REVERT: A  239 ASP cc_start: 0.8584 (m-30) cc_final: 0.8123 (m-30)
REVERT: A  240 PHE cc_start: 0.5541 (p90) cc_final: 0.4325 (m-80)
REVERT: B  116 LYS cc_start: 0.7221 (pmtt) cc_final: 0.6880 (ptmm)
REVERT: B  120 LEU cc_start: 0.8836 (mm) cc_final: 0.8383 (mp)
REVERT: B  124 GLN cc_start: 0.8047 (mp10) cc_final: 0.7731 (tm-30)
REVERT: B  135 PRO cc_start: 0.9390 (Cg_endo) cc_final: 0.8896 (Cg_exo)
REVERT: B  195 GLU cc_start: 0.7526 (tt0) cc_final: 0.7201 (tt0)
REVERT: B  202 GLU cc_start: 0.8164 (tp30) cc_final: 0.7841 (tp30)
REVERT: B  204 PHE cc_start: 0.8159 (m-80) cc_final: 0.7759 (m-10)
REVERT: B  226 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8899 (mmmt)
REVERT: B  236 ILE cc_start: 0.9192 (mt) cc_final: 0.8790 (tp)
REVERT: B  237 VAL cc_start: 0.8852 (m) cc_final: 0.8184 (p)
REVERT: B  239 ASP cc_start: 0.8776 (m-30) cc_final: 0.8456 (m-30)
  outliers start: 17
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2128
  time to fit residues: 30.3642
Evaluate side-chains
  129 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 21 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 2 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    5.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 235 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 = 0.3648 r_free = 0.3648 target = 0.108920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.087334 restraints weight = 7406.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.090094 restraints weight = 4216.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.091907 restraints weight = 2947.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.7403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079   2580  Z= 0.409
  Angle     :  1.035  13.799   3494  Z= 0.520
  Chirality :  0.059   0.202    388
  Planarity :  0.006   0.043    440
  Dihedral  :  6.819  22.833    336
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 29.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.25 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 29.51 %
    Favored  : 65.28 %
  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: -2.42 (0.50), residues: 302
  helix:  1.05 (0.64), residues: 72
  sheet: -2.04 (0.55), residues: 86
  loop : -2.78 (0.51), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 182 
 HIS   0.014   0.004   HIS A 110 
 PHE   0.025   0.002   PHE B 106 
 TYR   0.040   0.003   TYR A 126 
 ARG   0.010   0.001   ARG A 177 

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.8637 (m-30) cc_final: 0.8050 (m-30)
REVERT: A  139 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8029 (tp-100)
REVERT: A  197 GLN cc_start: 0.8043 (mp10) cc_final: 0.7725 (mp10)
REVERT: A  198 GLN cc_start: 0.8212 (mt0) cc_final: 0.7736 (mt0)
REVERT: A  211 ARG cc_start: 0.8711 (mmm-85) cc_final: 0.8462 (mmp80)
REVERT: A  230 TYR cc_start: 0.9200 (m-80) cc_final: 0.8726 (m-80)
REVERT: A  236 ILE cc_start: 0.9297 (mt) cc_final: 0.8737 (tp)
REVERT: A  237 VAL cc_start: 0.8940 (m) cc_final: 0.8309 (p)
REVERT: A  239 ASP cc_start: 0.8693 (m-30) cc_final: 0.8244 (m-30)
REVERT: A  240 PHE cc_start: 0.5631 (p90) cc_final: 0.4151 (m-80)
REVERT: B  116 LYS cc_start: 0.7116 (pmtt) cc_final: 0.6620 (ptmm)
REVERT: B  236 ILE cc_start: 0.9304 (mt) cc_final: 0.8794 (tp)
REVERT: B  237 VAL cc_start: 0.8912 (m) cc_final: 0.8199 (p)
REVERT: B  239 ASP cc_start: 0.8761 (m-30) cc_final: 0.8321 (m-30)
  outliers start: 15
  outliers final: 15
  residues processed: 120
  average time/residue: 0.2111
  time to fit residues: 28.2295
Evaluate side-chains
  126 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  221 GLU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0060
   chunk 5 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    3.4004

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 235 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 = 0.3717 r_free = 0.3717 target = 0.113076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.091224 restraints weight = 7022.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.094038 restraints weight = 3985.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.095928 restraints weight = 2739.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.7612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   2580  Z= 0.326
  Angle     :  1.019  12.361   3494  Z= 0.507
  Chirality :  0.057   0.203    388
  Planarity :  0.007   0.075    440
  Dihedral  :  6.746  22.768    336
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 26.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.91 %
    Favored  : 87.09 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 31.25 %
    Favored  : 63.19 %
  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: -2.32 (0.50), residues: 302
  helix:  1.12 (0.65), residues: 72
  sheet: -1.91 (0.57), residues: 86
  loop : -2.75 (0.51), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 192 
 HIS   0.014   0.003   HIS B 110 
 PHE   0.023   0.002   PHE B 106 
 TYR   0.033   0.002   TYR A 126 
 ARG   0.010   0.001   ARG A 177 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1275.22 seconds
wall clock time: 23 minutes 28.54 seconds (1408.54 seconds total)