Starting phenix.real_space_refine
on Wed Mar  5 16:01:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mlu_9146/03_2025/6mlu_9146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mlu_9146/03_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_9146/03_2025/6mlu_9146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mlu_9146/03_2025/6mlu_9146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mlu_9146/03_2025/6mlu_9146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mlu_9146/03_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-5624/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: 2.41, per 1000 atoms: 0.96
  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=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 149 " - pdb=" SG  CYS A 164 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 149 " - pdb=" SG  CYS B 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: 0.50
  Conformation dependent library (CDL) restraints added in 270.7 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: 0.29
  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: 0.61

  Time building geometry restraints manager: 0.63 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: 135
       22.73 -    34.09: 24
       34.09 -    45.46: 12
       45.46 -    56.82: 6
  Dihedral angle restraints: 1578
    sinusoidal: 664
      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 1575 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:
        2.41 -     2.90: 921
        2.90 -     3.40: 2472
        3.40 -     3.90: 4091
        3.90 -     4.40: 4488
        4.40 -     4.90: 7629
  Nonbonded interactions: 19601
  Sorted by model distance:
  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
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" N   TYR B 171 "
     model   vdw
     2.432 3.120
  ... (remaining 19596 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:             0.700
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.210
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.780
-------------------------------------------------------------------------------
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= 0.345
  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 : 2.406

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  : 0.312 
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: 0.2172
  time to fit residues: 39.2030
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  : 0.266 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    2.3188

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.111536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.089607 restraints weight = 7205.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.092411 restraints weight = 4063.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.094277 restraints weight = 2797.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.4264

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= 0.242
  Angle     :  0.818   7.403   3494  Z= 0.429
  Chirality :  0.054   0.203    388
  Planarity :  0.006   0.030    440
  Dihedral  :  6.264  23.418    336
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 16.32 %
    Favored  : 76.74 %
  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: -3.32 (0.46), residues: 302
  helix: -0.63 (0.57), residues: 74
  sheet: -1.83 (0.52), residues: 90
  loop : -3.40 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 192 
 HIS   0.010   0.002   HIS B 110 
 PHE   0.017   0.001   PHE B 106 
 TYR   0.008   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
  150 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8755 (pm20) cc_final: 0.8433 (pm20)
REVERT: A   95 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7967 (tppt)
REVERT: A   99 GLU cc_start: 0.8148 (pm20) cc_final: 0.7648 (pm20)
REVERT: A  116 LYS cc_start: 0.7754 (pmtt) cc_final: 0.7548 (ptmt)
REVERT: A  120 LEU cc_start: 0.8696 (mt) cc_final: 0.8337 (mt)
REVERT: A  124 GLN cc_start: 0.7128 (mp10) cc_final: 0.5781 (tm-30)
REVERT: A  133 ASP cc_start: 0.8691 (m-30) cc_final: 0.8162 (m-30)
REVERT: A  147 MET cc_start: 0.8210 (mmm) cc_final: 0.7505 (tpp)
REVERT: A  165 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7306 (mmt180)
REVERT: A  198 GLN cc_start: 0.8595 (mt0) cc_final: 0.8295 (mt0)
REVERT: A  202 GLU cc_start: 0.8439 (tt0) cc_final: 0.7958 (tm-30)
REVERT: A  204 PHE cc_start: 0.8148 (m-80) cc_final: 0.7469 (m-80)
REVERT: A  213 HIS cc_start: 0.7651 (m90) cc_final: 0.7394 (m-70)
REVERT: A  230 TYR cc_start: 0.9170 (m-80) cc_final: 0.8715 (m-80)
REVERT: A  236 ILE cc_start: 0.9257 (mt) cc_final: 0.9031 (tp)
REVERT: A  237 VAL cc_start: 0.9087 (m) cc_final: 0.8546 (p)
REVERT: A  239 ASP cc_start: 0.8759 (m-30) cc_final: 0.8278 (m-30)
REVERT: B  115 LYS cc_start: 0.7072 (ttmp) cc_final: 0.6679 (tptm)
REVERT: B  120 LEU cc_start: 0.8833 (mt) cc_final: 0.8367 (mm)
REVERT: B  127 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8155 (ptmt)
REVERT: B  133 ASP cc_start: 0.8531 (m-30) cc_final: 0.8293 (m-30)
REVERT: B  152 MET cc_start: 0.7456 (mmm) cc_final: 0.7073 (mmm)
REVERT: B  202 GLU cc_start: 0.8828 (tt0) cc_final: 0.8460 (tm-30)
REVERT: B  204 PHE cc_start: 0.8229 (m-80) cc_final: 0.7877 (m-10)
REVERT: B  211 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.7987 (mmp80)
REVERT: B  223 GLN cc_start: 0.8439 (mm110) cc_final: 0.7797 (mm-40)
REVERT: B  226 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8855 (mmmt)
REVERT: B  236 ILE cc_start: 0.9347 (mt) cc_final: 0.9013 (tp)
REVERT: B  237 VAL cc_start: 0.9087 (m) cc_final: 0.8189 (p)
REVERT: B  239 ASP cc_start: 0.8874 (m-30) cc_final: 0.8071 (p0)
  outliers start: 20
  outliers final: 10
  residues processed: 138
  average time/residue: 0.2018
  time to fit residues: 31.1439
Evaluate side-chains
  130 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  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  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:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 8 optimal weight:    0.0470
   chunk 13 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    3.4084

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.109009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.087968 restraints weight = 7280.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.090623 restraints weight = 4131.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.092386 restraints weight = 2867.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.5218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   2580  Z= 0.276
  Angle     :  0.791   7.217   3494  Z= 0.413
  Chirality :  0.054   0.222    388
  Planarity :  0.005   0.028    440
  Dihedral  :  6.171  22.812    336
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 21.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers : 10.76 %
    Allowed  : 21.18 %
    Favored  : 68.06 %
  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: -3.00 (0.47), residues: 302
  helix:  0.15 (0.59), residues: 74
  sheet: -2.15 (0.51), residues: 94
  loop : -3.11 (0.50), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 182 
 HIS   0.013   0.003   HIS A 110 
 PHE   0.020   0.002   PHE B 106 
 TYR   0.026   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
  153 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7932 (tppt)
REVERT: A  115 LYS cc_start: 0.7883 (tptm) cc_final: 0.7566 (mttm)
REVERT: A  116 LYS cc_start: 0.7667 (pmtt) cc_final: 0.7247 (tmtt)
REVERT: A  121 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.6115 (tpp)
REVERT: A  133 ASP cc_start: 0.8672 (m-30) cc_final: 0.8102 (m-30)
REVERT: A  136 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8304 (mp0)
REVERT: A  152 MET cc_start: 0.7120 (mmm) cc_final: 0.6803 (mmm)
REVERT: A  198 GLN cc_start: 0.8532 (mt0) cc_final: 0.8098 (mt0)
REVERT: A  204 PHE cc_start: 0.8166 (m-80) cc_final: 0.7705 (m-80)
REVERT: A  213 HIS cc_start: 0.7772 (m90) cc_final: 0.7502 (m-70)
REVERT: A  223 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8193 (mm-40)
REVERT: A  230 TYR cc_start: 0.9154 (m-80) cc_final: 0.8602 (m-80)
REVERT: A  236 ILE cc_start: 0.9288 (mt) cc_final: 0.8976 (tp)
REVERT: A  237 VAL cc_start: 0.9097 (m) cc_final: 0.8541 (p)
REVERT: A  239 ASP cc_start: 0.8736 (m-30) cc_final: 0.8303 (m-30)
REVERT: B  115 LYS cc_start: 0.7257 (ttmp) cc_final: 0.6792 (tptp)
REVERT: B  121 MET cc_start: 0.6709 (tmm) cc_final: 0.6382 (tpp)
REVERT: B  124 GLN cc_start: 0.8181 (mp10) cc_final: 0.7939 (tm-30)
REVERT: B  126 TYR cc_start: 0.7405 (m-80) cc_final: 0.7070 (m-80)
REVERT: B  127 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8151 (ptmt)
REVERT: B  136 GLU cc_start: 0.8757 (mp0) cc_final: 0.8401 (mp0)
REVERT: B  139 GLN cc_start: 0.8677 (tp40) cc_final: 0.8461 (tp-100)
REVERT: B  152 MET cc_start: 0.7565 (mmm) cc_final: 0.7189 (mmm)
REVERT: B  202 GLU cc_start: 0.8671 (tt0) cc_final: 0.8461 (tm-30)
REVERT: B  204 PHE cc_start: 0.8431 (m-80) cc_final: 0.7905 (m-10)
REVERT: B  211 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.7880 (mmp80)
REVERT: B  218 VAL cc_start: 0.9365 (m) cc_final: 0.9122 (t)
REVERT: B  236 ILE cc_start: 0.9316 (mt) cc_final: 0.8993 (tp)
REVERT: B  237 VAL cc_start: 0.9090 (m) cc_final: 0.8215 (p)
REVERT: B  239 ASP cc_start: 0.8880 (m-30) cc_final: 0.8017 (p0)
  outliers start: 31
  outliers final: 19
  residues processed: 134
  average time/residue: 0.1932
  time to fit residues: 28.9941
Evaluate side-chains
  134 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  121 MET
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  149 CYS
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:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    2.9586

-------------------------------------------------------------------------------
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 198 GLN ** 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 = 0.3685 r_free = 0.3685 target = 0.110014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.088334 restraints weight = 7308.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.090983 restraints weight = 4154.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.092723 restraints weight = 2884.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.5741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2580  Z= 0.251
  Angle     :  0.777   6.925   3494  Z= 0.403
  Chirality :  0.054   0.216    388
  Planarity :  0.005   0.036    440
  Dihedral  :  6.077  22.743    336
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 22.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  9.72 %
    Allowed  : 23.96 %
    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: -2.77 (0.47), residues: 302
  helix:  0.72 (0.60), residues: 72
  sheet: -2.08 (0.51), residues: 94
  loop : -3.12 (0.49), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 192 
 HIS   0.012   0.003   HIS A 110 
 PHE   0.019   0.002   PHE B 106 
 TYR   0.019   0.002   TYR A 126 
 ARG   0.002   0.000   ARG A  88 

*********************** 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
  140 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8815 (pp30) cc_final: 0.8583 (pm20)
REVERT: A  115 LYS cc_start: 0.7788 (tptm) cc_final: 0.7439 (mttm)
REVERT: A  116 LYS cc_start: 0.7839 (pmtt) cc_final: 0.7583 (ptmm)
REVERT: A  121 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6088 (tpt)
REVERT: A  133 ASP cc_start: 0.8646 (m-30) cc_final: 0.7938 (m-30)
REVERT: A  139 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7871 (tp-100)
REVERT: A  152 MET cc_start: 0.7273 (mmm) cc_final: 0.6974 (mmm)
REVERT: A  198 GLN cc_start: 0.8467 (mt0) cc_final: 0.7875 (mt0)
REVERT: A  213 HIS cc_start: 0.7615 (m90) cc_final: 0.7344 (m-70)
REVERT: A  221 GLU cc_start: 0.8087 (pt0) cc_final: 0.7881 (tm-30)
REVERT: A  230 TYR cc_start: 0.9172 (m-80) cc_final: 0.8748 (m-80)
REVERT: A  236 ILE cc_start: 0.9276 (mt) cc_final: 0.8789 (tp)
REVERT: A  237 VAL cc_start: 0.9017 (m) cc_final: 0.8343 (p)
REVERT: A  239 ASP cc_start: 0.8858 (m-30) cc_final: 0.8216 (m-30)
REVERT: B  115 LYS cc_start: 0.7404 (ttmp) cc_final: 0.6742 (tptp)
REVERT: B  116 LYS cc_start: 0.7098 (pmtt) cc_final: 0.6531 (ptmm)
REVERT: B  120 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8483 (mm)
REVERT: B  124 GLN cc_start: 0.8261 (mp10) cc_final: 0.7982 (tm-30)
REVERT: B  126 TYR cc_start: 0.7187 (m-80) cc_final: 0.6674 (m-80)
REVERT: B  136 GLU cc_start: 0.8690 (mp0) cc_final: 0.8240 (mp0)
REVERT: B  236 ILE cc_start: 0.9287 (mt) cc_final: 0.8992 (tp)
REVERT: B  237 VAL cc_start: 0.9082 (m) cc_final: 0.8559 (p)
REVERT: B  239 ASP cc_start: 0.8870 (m-30) cc_final: 0.8447 (m-30)
  outliers start: 28
  outliers final: 18
  residues processed: 123
  average time/residue: 0.2006
  time to fit residues: 27.7930
Evaluate side-chains
  127 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
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  120 LEU
Chi-restraints excluded: chain A residue  121 MET
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  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  120 LEU
Chi-restraints excluded: chain B residue  149 CYS
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:    0.7980
   chunk 20 optimal weight:    8.9990
   chunk 16 optimal weight:    0.0020
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 7 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    2.3594

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 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 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 = 0.3715 r_free = 0.3715 target = 0.111772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.090228 restraints weight = 7078.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.092996 restraints weight = 3895.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.094781 restraints weight = 2660.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.6114

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= 0.246
  Angle     :  0.781   7.118   3494  Z= 0.402
  Chirality :  0.054   0.210    388
  Planarity :  0.005   0.032    440
  Dihedral  :  6.070  22.171    336
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers : 10.76 %
    Allowed  : 23.61 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.48), residues: 302
  helix:  0.98 (0.62), residues: 72
  sheet: -1.99 (0.51), residues: 94
  loop : -3.00 (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 A 110 
 PHE   0.019   0.002   PHE B 106 
 TYR   0.016   0.002   TYR A 126 
 ARG   0.003   0.000   ARG A 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
  146 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7862 (tptm) cc_final: 0.7513 (mttm)
REVERT: A  121 MET cc_start: 0.6434 (OUTLIER) cc_final: 0.6056 (tpt)
REVERT: A  133 ASP cc_start: 0.8619 (m-30) cc_final: 0.7958 (m-30)
REVERT: A  136 GLU cc_start: 0.8677 (mp0) cc_final: 0.7171 (mp0)
REVERT: A  139 GLN cc_start: 0.8285 (tp-100) cc_final: 0.8047 (tp40)
REVERT: A  193 LYS cc_start: 0.7562 (mmtm) cc_final: 0.7039 (mmtp)
REVERT: A  195 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7065 (mt-10)
REVERT: A  198 GLN cc_start: 0.8370 (mt0) cc_final: 0.7745 (mt0)
REVERT: A  211 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8175 (mtp85)
REVERT: A  213 HIS cc_start: 0.7356 (m90) cc_final: 0.7073 (m-70)
REVERT: A  221 GLU cc_start: 0.8115 (pt0) cc_final: 0.7834 (tm-30)
REVERT: A  230 TYR cc_start: 0.9152 (m-80) cc_final: 0.8803 (m-80)
REVERT: A  236 ILE cc_start: 0.9204 (mt) cc_final: 0.8784 (tp)
REVERT: A  237 VAL cc_start: 0.9018 (m) cc_final: 0.8282 (p)
REVERT: A  239 ASP cc_start: 0.8805 (m-30) cc_final: 0.8140 (m-30)
REVERT: B  115 LYS cc_start: 0.7515 (ttmp) cc_final: 0.6780 (tptp)
REVERT: B  116 LYS cc_start: 0.7052 (pmtt) cc_final: 0.6530 (ptmm)
REVERT: B  120 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8424 (mp)
REVERT: B  124 GLN cc_start: 0.8251 (mp10) cc_final: 0.7912 (tm-30)
REVERT: B  126 TYR cc_start: 0.6702 (m-10) cc_final: 0.6329 (m-80)
REVERT: B  136 GLU cc_start: 0.8706 (mp0) cc_final: 0.8405 (mp0)
REVERT: B  152 MET cc_start: 0.7403 (mmm) cc_final: 0.7060 (mmm)
REVERT: B  204 PHE cc_start: 0.8173 (m-80) cc_final: 0.7903 (m-10)
REVERT: B  211 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7557 (mmp80)
REVERT: B  236 ILE cc_start: 0.9256 (mt) cc_final: 0.8904 (tp)
REVERT: B  237 VAL cc_start: 0.9034 (m) cc_final: 0.8528 (p)
REVERT: B  239 ASP cc_start: 0.8861 (m-30) cc_final: 0.8448 (m-30)
  outliers start: 31
  outliers final: 20
  residues processed: 128
  average time/residue: 0.1938
  time to fit residues: 27.8448
Evaluate side-chains
  134 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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  121 MET
Chi-restraints excluded: chain A residue  127 LYS
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  169 MET
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  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:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    8.9990
   chunk 24 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0170
   chunk 16 optimal weight:    0.0980
   chunk 7 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    2.3622

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.111676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.090551 restraints weight = 7176.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.093340 restraints weight = 3982.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.095170 restraints weight = 2718.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.6378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   2580  Z= 0.246
  Angle     :  0.795   6.849   3494  Z= 0.411
  Chirality :  0.053   0.205    388
  Planarity :  0.005   0.034    440
  Dihedral  :  6.005  23.322    336
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 22.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.93 %
    Favored  : 89.07 %
  Rotamer:
    Outliers : 10.07 %
    Allowed  : 23.96 %
    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: -2.47 (0.47), residues: 302
  helix:  1.22 (0.62), residues: 72
  sheet: -1.79 (0.52), residues: 82
  loop : -3.13 (0.48), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 182 
 HIS   0.012   0.002   HIS B 110 
 PHE   0.019   0.002   PHE B 106 
 TYR   0.013   0.002   TYR B 126 
 ARG   0.003   0.000   ARG A 211 

*********************** 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
  147 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7777 (tptm) cc_final: 0.7423 (mttm)
REVERT: A  121 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.6047 (tpt)
REVERT: A  133 ASP cc_start: 0.8621 (m-30) cc_final: 0.8129 (m-30)
REVERT: A  193 LYS cc_start: 0.7549 (mmtm) cc_final: 0.6962 (mmtp)
REVERT: A  197 GLN cc_start: 0.7645 (mp10) cc_final: 0.7190 (mp-120)
REVERT: A  198 GLN cc_start: 0.8463 (mt0) cc_final: 0.8019 (mt0)
REVERT: A  211 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8122 (mtp85)
REVERT: A  213 HIS cc_start: 0.7477 (m90) cc_final: 0.7233 (m-70)
REVERT: A  223 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8091 (mm-40)
REVERT: A  230 TYR cc_start: 0.9151 (m-80) cc_final: 0.8690 (m-80)
REVERT: A  236 ILE cc_start: 0.9235 (mt) cc_final: 0.8604 (tp)
REVERT: A  237 VAL cc_start: 0.9006 (m) cc_final: 0.8280 (p)
REVERT: A  239 ASP cc_start: 0.8816 (m-30) cc_final: 0.8188 (m-30)
REVERT: B  116 LYS cc_start: 0.7030 (pmtt) cc_final: 0.6558 (ptmm)
REVERT: B  120 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8472 (mp)
REVERT: B  124 GLN cc_start: 0.8259 (mp10) cc_final: 0.7950 (tm-30)
REVERT: B  126 TYR cc_start: 0.6690 (m-10) cc_final: 0.6351 (m-80)
REVERT: B  135 PRO cc_start: 0.9535 (Cg_endo) cc_final: 0.9125 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8670 (mp0) cc_final: 0.8439 (mp0)
REVERT: B  152 MET cc_start: 0.7689 (mmm) cc_final: 0.7222 (mmm)
REVERT: B  195 GLU cc_start: 0.7327 (tt0) cc_final: 0.6944 (tt0)
REVERT: B  204 PHE cc_start: 0.8184 (m-80) cc_final: 0.7842 (m-10)
REVERT: B  211 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.7572 (mmp80)
REVERT: B  226 LYS cc_start: 0.9361 (mmmm) cc_final: 0.9022 (mmmt)
REVERT: B  236 ILE cc_start: 0.9180 (mt) cc_final: 0.8862 (tp)
REVERT: B  237 VAL cc_start: 0.9012 (m) cc_final: 0.8473 (p)
REVERT: B  239 ASP cc_start: 0.8827 (m-30) cc_final: 0.8336 (m-30)
  outliers start: 29
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1966
  time to fit residues: 28.0249
Evaluate side-chains
  135 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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  121 MET
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  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  120 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  149 CYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:   20.0000
   chunk 28 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.7784

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.113547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.091874 restraints weight = 6985.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.094593 restraints weight = 3822.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.096386 restraints weight = 2610.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.6693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   2580  Z= 0.236
  Angle     :  0.854  10.247   3494  Z= 0.431
  Chirality :  0.054   0.215    388
  Planarity :  0.005   0.036    440
  Dihedral  :  5.979  23.367    336
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 21.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  7.99 %
    Allowed  : 27.43 %
    Favored  : 64.58 %
  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: -2.49 (0.48), residues: 302
  helix:  0.98 (0.61), residues: 72
  sheet: -1.66 (0.53), residues: 82
  loop : -3.10 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 192 
 HIS   0.012   0.002   HIS B 110 
 PHE   0.017   0.002   PHE B 106 
 TYR   0.011   0.001   TYR B 126 
 ARG   0.003   0.000   ARG A 177 

*********************** 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: 23
    poor density    : 124
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7752 (tptm) cc_final: 0.7430 (mttm)
REVERT: A  121 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.6040 (tpt)
REVERT: A  133 ASP cc_start: 0.8567 (m-30) cc_final: 0.8044 (m-30)
REVERT: A  136 GLU cc_start: 0.8189 (mp0) cc_final: 0.7741 (mp0)
REVERT: A  193 LYS cc_start: 0.7455 (mmtm) cc_final: 0.6684 (mmtp)
REVERT: A  198 GLN cc_start: 0.8335 (mt0) cc_final: 0.7925 (mt0)
REVERT: A  213 HIS cc_start: 0.7481 (m90) cc_final: 0.7250 (m90)
REVERT: A  221 GLU cc_start: 0.8094 (pt0) cc_final: 0.7894 (tm-30)
REVERT: A  230 TYR cc_start: 0.9075 (m-80) cc_final: 0.8694 (m-80)
REVERT: A  232 VAL cc_start: 0.9401 (t) cc_final: 0.9118 (m)
REVERT: A  236 ILE cc_start: 0.9287 (mt) cc_final: 0.8650 (tp)
REVERT: A  239 ASP cc_start: 0.8774 (m-30) cc_final: 0.8510 (m-30)
REVERT: B  116 LYS cc_start: 0.7099 (pmtt) cc_final: 0.6704 (ptmm)
REVERT: B  120 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8504 (mp)
REVERT: B  124 GLN cc_start: 0.8237 (mp10) cc_final: 0.7956 (tm-30)
REVERT: B  126 TYR cc_start: 0.6497 (m-10) cc_final: 0.6228 (m-80)
REVERT: B  135 PRO cc_start: 0.9510 (Cg_endo) cc_final: 0.9089 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8645 (mp0) cc_final: 0.8326 (mp0)
REVERT: B  146 PHE cc_start: 0.8895 (p90) cc_final: 0.8608 (p90)
REVERT: B  152 MET cc_start: 0.7999 (mmm) cc_final: 0.7637 (mmm)
REVERT: B  195 GLU cc_start: 0.7309 (tt0) cc_final: 0.6812 (tt0)
REVERT: B  204 PHE cc_start: 0.8089 (m-80) cc_final: 0.7884 (m-10)
REVERT: B  211 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.8095 (mtp85)
REVERT: B  221 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6538 (pp20)
REVERT: B  223 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8038 (mm-40)
REVERT: B  226 LYS cc_start: 0.9342 (mmmm) cc_final: 0.9024 (mmmt)
REVERT: B  236 ILE cc_start: 0.9228 (mt) cc_final: 0.8848 (tp)
REVERT: B  237 VAL cc_start: 0.8988 (m) cc_final: 0.8088 (p)
REVERT: B  239 ASP cc_start: 0.8841 (m-30) cc_final: 0.8253 (m-30)
  outliers start: 23
  outliers final: 16
  residues processed: 132
  average time/residue: 0.2078
  time to fit residues: 30.7557
Evaluate side-chains
  135 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  121 MET
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   94 PHE
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  149 CYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 2 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 3 optimal weight:   20.0000
   chunk 18 optimal weight:    9.9990
   overall best weight:    3.7990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.110569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.087771 restraints weight = 7358.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.090462 restraints weight = 4231.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.092271 restraints weight = 2995.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.7006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   2580  Z= 0.309
  Angle     :  0.924  13.257   3494  Z= 0.466
  Chirality :  0.056   0.206    388
  Planarity :  0.005   0.031    440
  Dihedral  :  6.242  23.150    336
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 26.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  9.38 %
    Allowed  : 25.00 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.48), residues: 302
  helix:  0.90 (0.63), residues: 72
  sheet: -1.74 (0.55), residues: 82
  loop : -3.00 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 192 
 HIS   0.013   0.003   HIS B 110 
 PHE   0.021   0.002   PHE B 106 
 TYR   0.012   0.002   TYR B 126 
 ARG   0.004   0.001   ARG A 177 

*********************** 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: 27
    poor density    : 117
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9107 (pp30) cc_final: 0.8857 (pp30)
REVERT: A  115 LYS cc_start: 0.7791 (tptm) cc_final: 0.7250 (mttm)
REVERT: A  121 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.5987 (tpt)
REVERT: A  133 ASP cc_start: 0.8616 (m-30) cc_final: 0.8009 (m-30)
REVERT: A  198 GLN cc_start: 0.8116 (mt0) cc_final: 0.7728 (mt0)
REVERT: A  202 GLU cc_start: 0.7913 (tp30) cc_final: 0.7617 (tp30)
REVERT: A  213 HIS cc_start: 0.7564 (m90) cc_final: 0.7327 (m-70)
REVERT: A  230 TYR cc_start: 0.9090 (m-80) cc_final: 0.8675 (m-80)
REVERT: A  232 VAL cc_start: 0.9188 (t) cc_final: 0.8786 (t)
REVERT: A  236 ILE cc_start: 0.9239 (mt) cc_final: 0.8735 (tp)
REVERT: A  239 ASP cc_start: 0.8831 (m-30) cc_final: 0.8571 (m-30)
REVERT: B  116 LYS cc_start: 0.6984 (pmtt) cc_final: 0.6488 (ptmm)
REVERT: B  120 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8480 (mp)
REVERT: B  124 GLN cc_start: 0.8299 (mp10) cc_final: 0.7961 (tm-30)
REVERT: B  126 TYR cc_start: 0.6219 (m-10) cc_final: 0.5914 (m-80)
REVERT: B  135 PRO cc_start: 0.9504 (Cg_endo) cc_final: 0.9095 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8631 (mp0) cc_final: 0.8407 (mp0)
REVERT: B  146 PHE cc_start: 0.8712 (p90) cc_final: 0.8450 (p90)
REVERT: B  152 MET cc_start: 0.8225 (mmm) cc_final: 0.7914 (mmm)
REVERT: B  195 GLU cc_start: 0.7493 (tt0) cc_final: 0.7241 (tt0)
REVERT: B  204 PHE cc_start: 0.8114 (m-80) cc_final: 0.7911 (m-10)
REVERT: B  221 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6813 (pp20)
REVERT: B  223 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8069 (mm-40)
REVERT: B  236 ILE cc_start: 0.9189 (mt) cc_final: 0.8849 (tp)
REVERT: B  237 VAL cc_start: 0.8985 (m) cc_final: 0.8394 (p)
REVERT: B  239 ASP cc_start: 0.8901 (m-30) cc_final: 0.8417 (m-30)
  outliers start: 27
  outliers final: 21
  residues processed: 128
  average time/residue: 0.1846
  time to fit residues: 26.9587
Evaluate side-chains
  137 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 HIS
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  121 MET
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  156 ASP
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   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  149 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    8.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
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**
B 235 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.114359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.092433 restraints weight = 7020.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.095176 restraints weight = 3949.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.096939 restraints weight = 2760.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.7264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   2580  Z= 0.261
  Angle     :  0.960  12.531   3494  Z= 0.474
  Chirality :  0.056   0.257    388
  Planarity :  0.005   0.034    440
  Dihedral  :  6.228  23.009    336
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 21.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.58 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  7.99 %
    Allowed  : 26.39 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.49), residues: 302
  helix:  0.64 (0.62), residues: 72
  sheet: -1.65 (0.56), residues: 82
  loop : -2.83 (0.51), 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   0.019   0.002   PHE B 106 
 TYR   0.011   0.001   TYR B 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
  143 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7911 (tppt)
REVERT: A  115 LYS cc_start: 0.7680 (tptm) cc_final: 0.7192 (mttm)
REVERT: A  121 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6263 (tpt)
REVERT: A  133 ASP cc_start: 0.8591 (m-30) cc_final: 0.7930 (m-30)
REVERT: A  193 LYS cc_start: 0.7087 (mmtm) cc_final: 0.6676 (mmtp)
REVERT: A  198 GLN cc_start: 0.7980 (mt0) cc_final: 0.7524 (mt0)
REVERT: A  211 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8049 (mmp-170)
REVERT: A  223 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8089 (mm-40)
REVERT: A  230 TYR cc_start: 0.9079 (m-80) cc_final: 0.8613 (m-80)
REVERT: A  232 VAL cc_start: 0.9350 (t) cc_final: 0.9051 (m)
REVERT: A  236 ILE cc_start: 0.9263 (mt) cc_final: 0.8736 (tp)
REVERT: A  239 ASP cc_start: 0.8747 (m-30) cc_final: 0.8485 (m-30)
REVERT: B  116 LYS cc_start: 0.7016 (pmtt) cc_final: 0.6519 (ptmm)
REVERT: B  120 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8592 (mp)
REVERT: B  124 GLN cc_start: 0.8172 (mp10) cc_final: 0.7935 (tm-30)
REVERT: B  126 TYR cc_start: 0.6282 (m-10) cc_final: 0.5624 (m-80)
REVERT: B  135 PRO cc_start: 0.9358 (Cg_endo) cc_final: 0.8937 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8647 (mp0) cc_final: 0.8334 (mp0)
REVERT: B  145 MET cc_start: 0.7543 (mtm) cc_final: 0.7276 (mtm)
REVERT: B  152 MET cc_start: 0.7698 (mmm) cc_final: 0.7382 (mmm)
REVERT: B  168 MET cc_start: 0.7463 (ptm) cc_final: 0.7205 (ppp)
REVERT: B  195 GLU cc_start: 0.7485 (tt0) cc_final: 0.7054 (tt0)
REVERT: B  212 GLN cc_start: 0.8745 (mp10) cc_final: 0.8410 (mp10)
REVERT: B  226 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8823 (mmmt)
REVERT: B  236 ILE cc_start: 0.9144 (mt) cc_final: 0.8769 (tp)
REVERT: B  237 VAL cc_start: 0.8937 (m) cc_final: 0.8193 (p)
REVERT: B  239 ASP cc_start: 0.8947 (m-30) cc_final: 0.8484 (m-30)
  outliers start: 23
  outliers final: 18
  residues processed: 127
  average time/residue: 0.1783
  time to fit residues: 25.6332
Evaluate side-chains
  135 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 HIS
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  121 MET
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  156 ASP
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  106 PHE
Chi-restraints excluded: chain B residue  113 LEU
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  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:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.113830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.092059 restraints weight = 7076.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.094768 restraints weight = 3931.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.096554 restraints weight = 2722.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.7489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   2580  Z= 0.337
  Angle     :  1.076  13.108   3494  Z= 0.518
  Chirality :  0.061   0.261    388
  Planarity :  0.006   0.044    440
  Dihedral  :  6.478  22.653    336
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 26.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.91 %
    Favored  : 86.09 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 27.78 %
    Favored  : 63.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.50), residues: 302
  helix:  0.96 (0.65), residues: 72
  sheet: -1.99 (0.53), residues: 86
  loop : -2.84 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 192 
 HIS   0.013   0.003   HIS B 110 
 PHE   0.036   0.003   PHE B 204 
 TYR   0.008   0.001   TYR B 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
  139 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7807 (tptm) cc_final: 0.7353 (mttm)
REVERT: A  121 MET cc_start: 0.6632 (tpp) cc_final: 0.6177 (tpt)
REVERT: A  133 ASP cc_start: 0.8620 (m-30) cc_final: 0.7987 (m-30)
REVERT: A  193 LYS cc_start: 0.7149 (mmtm) cc_final: 0.6759 (mmtp)
REVERT: A  198 GLN cc_start: 0.7954 (mt0) cc_final: 0.7493 (mt0)
REVERT: A  211 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.8111 (mmp-170)
REVERT: A  223 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8548 (mm-40)
REVERT: A  230 TYR cc_start: 0.9154 (m-80) cc_final: 0.8691 (m-80)
REVERT: A  232 VAL cc_start: 0.9278 (t) cc_final: 0.9055 (m)
REVERT: A  236 ILE cc_start: 0.9285 (mt) cc_final: 0.8701 (tp)
REVERT: A  239 ASP cc_start: 0.8768 (m-30) cc_final: 0.8540 (m-30)
REVERT: B  116 LYS cc_start: 0.7065 (pmtt) cc_final: 0.6544 (ptmm)
REVERT: B  120 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8660 (mp)
REVERT: B  124 GLN cc_start: 0.8239 (mp10) cc_final: 0.7921 (tm-30)
REVERT: B  126 TYR cc_start: 0.5927 (m-10) cc_final: 0.4874 (m-80)
REVERT: B  135 PRO cc_start: 0.9379 (Cg_endo) cc_final: 0.8903 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8676 (mp0) cc_final: 0.8461 (mp0)
REVERT: B  168 MET cc_start: 0.7514 (ptm) cc_final: 0.7198 (ppp)
REVERT: B  195 GLU cc_start: 0.7562 (tt0) cc_final: 0.7182 (tt0)
REVERT: B  212 GLN cc_start: 0.8730 (mp10) cc_final: 0.8419 (mp10)
REVERT: B  226 LYS cc_start: 0.9336 (mmmm) cc_final: 0.8994 (mmmt)
REVERT: B  236 ILE cc_start: 0.9212 (mt) cc_final: 0.8860 (tp)
REVERT: B  239 ASP cc_start: 0.8975 (m-30) cc_final: 0.8648 (m-30)
  outliers start: 24
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1839
  time to fit residues: 25.8062
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  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 HIS
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  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 B residue   94 PHE
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  113 LEU
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  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 0 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0050
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 139 GLN
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 118 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 = 0.3834 r_free = 0.3834 target = 0.121952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.099319 restraints weight = 6918.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.102079 restraints weight = 3903.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.103809 restraints weight = 2726.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.7849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   2580  Z= 0.285
  Angle     :  1.011  12.830   3494  Z= 0.492
  Chirality :  0.058   0.269    388
  Planarity :  0.006   0.053    440
  Dihedral  :  6.154  22.286    336
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 20.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.92 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 31.25 %
    Favored  : 63.54 %
  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: -2.60 (0.49), residues: 302
  helix:  0.61 (0.63), residues: 72
  sheet: -1.80 (0.54), residues: 86
  loop : -2.97 (0.52), residues: 144

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   0.029   0.002   PHE B 204 
 TYR   0.009   0.001   TYR A 155 
 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: 1289.01 seconds
wall clock time: 22 minutes 55.85 seconds (1375.85 seconds total)