Starting phenix.real_space_refine
on Tue Mar  3 11:04:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mlu_9146/03_2026/6mlu_9146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mlu_9146/03_2026/6mlu_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mlu_9146/03_2026/6mlu_9146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mlu_9146/03_2026/6mlu_9146.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mlu_9146/03_2026/6mlu_9146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mlu_9146/03_2026/6mlu_9146.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.81, per 1000 atoms: 0.32
  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: 0.15
  Conformation dependent library (CDL) restraints added in 101.0 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: 0.10
  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: 0.26

  Time building geometry restraints manager: 0.20 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: 0.00
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:             1.110
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.560
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
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   2582  Z= 0.254
  Angle     :  1.047  10.429   3498  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG A 177 
 TYR   0.008   0.002   TYR B 155 
 PHE   0.015   0.003   PHE A 196 
 TRP   0.008   0.002   TRP B 192 
 HIS   0.013   0.004   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 2580)
  covalent geometry    : angle       1.04648 ( 3494)
  SS BOND              : bond        0.00789 (    2)
  SS BOND              : angle       1.37210 (    4)
  hydrogen bonds       : bond        0.22988 (   94)
  hydrogen bonds       : angle       8.86066 (  300)

*********************** 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  : 0.097 
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: 0.8305 (mmm) cc_final: 0.7640 (tpp)
REVERT: A  165 ARG cc_start: 0.7551 (mmt-90) cc_final: 0.7122 (mmt180)
REVERT: A  177 ARG cc_start: 0.8239 (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: 0.8826 (mt0) cc_final: 0.8598 (mp-120)
REVERT: A  198 GLN cc_start: 0.8747 (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: 0.9658 (t) cc_final: 0.8480 (t)
REVERT: A  236 ILE cc_start: 0.9237 (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: 0.8411 (m-30)
REVERT: B  177 ARG cc_start: 0.8291 (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: 0.0925
  time to fit residues: 16.7702
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  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.112052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.090020 restraints weight = 7196.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.092810 restraints weight = 4081.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.094681 restraints weight = 2812.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.095929 restraints weight = 2193.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.096707 restraints weight = 1865.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2582  Z= 0.176
  Angle     :  0.814   7.376   3498  Z= 0.427
  Chirality :  0.054   0.201    388
  Planarity :  0.006   0.030    440
  Dihedral  :  6.233  23.279    336
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  7.29 %
    Allowed  : 15.62 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.33 (0.46), residues: 302
  helix: -0.64 (0.57), residues: 74
  sheet: -1.81 (0.53), residues: 90
  loop : -3.41 (0.48), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  88 
 TYR   0.008   0.001   TYR A 219 
 PHE   0.017   0.002   PHE B 106 
 TRP   0.007   0.001   TRP B 192 
 HIS   0.010   0.002   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 2580)
  covalent geometry    : angle       0.81256 ( 3494)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       1.48827 (    4)
  hydrogen bonds       : bond        0.05197 (   94)
  hydrogen bonds       : angle       6.03674 (  300)

*********************** 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
  151 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8787 (pm20) cc_final: 0.8452 (pm20)
REVERT: A   95 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7969 (tppt)
REVERT: A  120 LEU cc_start: 0.8655 (mt) cc_final: 0.8306 (mt)
REVERT: A  124 GLN cc_start: 0.7211 (mp10) cc_final: 0.5897 (tm-30)
REVERT: A  133 ASP cc_start: 0.8661 (m-30) cc_final: 0.8151 (m-30)
REVERT: A  147 MET cc_start: 0.8186 (mmm) cc_final: 0.7481 (tpp)
REVERT: A  165 ARG cc_start: 0.8133 (mmt-90) cc_final: 0.7295 (mmt180)
REVERT: A  198 GLN cc_start: 0.8593 (mt0) cc_final: 0.8302 (mt0)
REVERT: A  202 GLU cc_start: 0.8453 (tt0) cc_final: 0.7940 (tm-30)
REVERT: A  204 PHE cc_start: 0.8192 (m-80) cc_final: 0.7505 (m-80)
REVERT: A  213 HIS cc_start: 0.7528 (m90) cc_final: 0.7269 (m-70)
REVERT: A  230 TYR cc_start: 0.9164 (m-80) cc_final: 0.8706 (m-80)
REVERT: A  236 ILE cc_start: 0.9235 (mt) cc_final: 0.9030 (tp)
REVERT: A  237 VAL cc_start: 0.9080 (m) cc_final: 0.8529 (p)
REVERT: A  239 ASP cc_start: 0.8711 (m-30) cc_final: 0.8235 (m-30)
REVERT: B  115 LYS cc_start: 0.7133 (ttmp) cc_final: 0.6769 (tptm)
REVERT: B  120 LEU cc_start: 0.8833 (mt) cc_final: 0.8362 (mm)
REVERT: B  121 MET cc_start: 0.7141 (tmm) cc_final: 0.6883 (tpp)
REVERT: B  127 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8024 (ptmt)
REVERT: B  152 MET cc_start: 0.7432 (mmm) cc_final: 0.7053 (mmm)
REVERT: B  195 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6921 (mt-10)
REVERT: B  198 GLN cc_start: 0.8257 (mt0) cc_final: 0.8056 (tt0)
REVERT: B  202 GLU cc_start: 0.8810 (tt0) cc_final: 0.8449 (tm-30)
REVERT: B  204 PHE cc_start: 0.8208 (m-80) cc_final: 0.7870 (m-10)
REVERT: B  211 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7993 (mmp80)
REVERT: B  223 GLN cc_start: 0.8386 (mm110) cc_final: 0.7683 (mm-40)
REVERT: B  236 ILE cc_start: 0.9334 (mt) cc_final: 0.8995 (tp)
REVERT: B  237 VAL cc_start: 0.9071 (m) cc_final: 0.8145 (p)
REVERT: B  239 ASP cc_start: 0.8847 (m-30) cc_final: 0.8088 (p0)
  outliers start: 21
  outliers final: 10
  residues processed: 138
  average time/residue: 0.0738
  time to fit residues: 11.4647
Evaluate side-chains
  132 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
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 14 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 12 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    3.5588

-------------------------------------------------------------------------------
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 197 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.109071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.087830 restraints weight = 7369.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.090518 restraints weight = 4125.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.092318 restraints weight = 2849.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.093488 restraints weight = 2228.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.094225 restraints weight = 1898.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.5267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2582  Z= 0.197
  Angle     :  0.799   7.301   3498  Z= 0.418
  Chirality :  0.054   0.225    388
  Planarity :  0.005   0.026    440
  Dihedral  :  6.177  22.579    336
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 21.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  9.03 %
    Allowed  : 22.22 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.47), residues: 302
  helix:  0.21 (0.59), residues: 74
  sheet: -2.12 (0.51), residues: 94
  loop : -3.10 (0.50), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  88 
 TYR   0.024   0.002   TYR B 126 
 PHE   0.019   0.002   PHE A 106 
 TRP   0.004   0.001   TRP A 182 
 HIS   0.013   0.003   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 2580)
  covalent geometry    : angle       0.79717 ( 3494)
  SS BOND              : bond        0.00087 (    2)
  SS BOND              : angle       1.58660 (    4)
  hydrogen bonds       : bond        0.04457 (   94)
  hydrogen bonds       : angle       5.98631 (  300)

*********************** 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
  145 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8001 (tppt)
REVERT: A  115 LYS cc_start: 0.7882 (tptm) cc_final: 0.7404 (mttm)
REVERT: A  121 MET cc_start: 0.6820 (tpp) cc_final: 0.6571 (tpt)
REVERT: A  133 ASP cc_start: 0.8699 (m-30) cc_final: 0.8141 (m-30)
REVERT: A  136 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8308 (mp0)
REVERT: A  152 MET cc_start: 0.7112 (mmm) cc_final: 0.6788 (mmm)
REVERT: A  198 GLN cc_start: 0.8547 (mt0) cc_final: 0.8123 (mt0)
REVERT: A  204 PHE cc_start: 0.8196 (m-80) cc_final: 0.7736 (m-80)
REVERT: A  213 HIS cc_start: 0.7671 (m90) cc_final: 0.7414 (m-70)
REVERT: A  223 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8164 (mm-40)
REVERT: A  230 TYR cc_start: 0.9160 (m-80) cc_final: 0.8631 (m-80)
REVERT: A  236 ILE cc_start: 0.9300 (mt) cc_final: 0.8909 (tp)
REVERT: A  237 VAL cc_start: 0.9087 (m) cc_final: 0.8457 (p)
REVERT: A  239 ASP cc_start: 0.8666 (m-30) cc_final: 0.8174 (m-30)
REVERT: B  115 LYS cc_start: 0.7264 (ttmp) cc_final: 0.6810 (tptp)
REVERT: B  120 LEU cc_start: 0.8729 (mt) cc_final: 0.8512 (mm)
REVERT: B  121 MET cc_start: 0.7099 (tmm) cc_final: 0.6872 (tpp)
REVERT: B  124 GLN cc_start: 0.8105 (mp10) cc_final: 0.7843 (tm-30)
REVERT: B  126 TYR cc_start: 0.7376 (m-80) cc_final: 0.7014 (m-80)
REVERT: B  127 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8172 (ptmt)
REVERT: B  136 GLU cc_start: 0.8826 (mp0) cc_final: 0.8441 (mp0)
REVERT: B  195 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7255 (mt-10)
REVERT: B  218 VAL cc_start: 0.9326 (m) cc_final: 0.9064 (t)
REVERT: B  236 ILE cc_start: 0.9325 (mt) cc_final: 0.9046 (tp)
REVERT: B  237 VAL cc_start: 0.9097 (m) cc_final: 0.8180 (p)
REVERT: B  239 ASP cc_start: 0.8818 (m-30) cc_final: 0.7999 (p0)
  outliers start: 26
  outliers final: 18
  residues processed: 131
  average time/residue: 0.0669
  time to fit residues: 9.9268
Evaluate side-chains
  131 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  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  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  190 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 6 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 11 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:   40.0000
   chunk 12 optimal weight:    7.9990
   overall best weight:    3.0984

-------------------------------------------------------------------------------
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 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.110954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.089161 restraints weight = 7352.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.091959 restraints weight = 4170.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.093784 restraints weight = 2871.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.094978 restraints weight = 2259.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.095695 restraints weight = 1923.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.5694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2582  Z= 0.175
  Angle     :  0.780   6.856   3498  Z= 0.407
  Chirality :  0.053   0.219    388
  Planarity :  0.005   0.029    440
  Dihedral  :  6.080  23.643    336
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 20.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  9.38 %
    Allowed  : 22.57 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.47), residues: 302
  helix:  0.66 (0.60), residues: 74
  sheet: -2.10 (0.51), residues: 94
  loop : -2.94 (0.50), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 211 
 TYR   0.021   0.002   TYR A 126 
 PHE   0.018   0.002   PHE B 106 
 TRP   0.005   0.001   TRP A 192 
 HIS   0.013   0.003   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 2580)
  covalent geometry    : angle       0.77879 ( 3494)
  SS BOND              : bond        0.00044 (    2)
  SS BOND              : angle       1.50934 (    4)
  hydrogen bonds       : bond        0.03983 (   94)
  hydrogen bonds       : angle       6.00006 (  300)

*********************** 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
  142 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7743 (tptm) cc_final: 0.7417 (mttm)
REVERT: A  121 MET cc_start: 0.6391 (tpp) cc_final: 0.6025 (tpt)
REVERT: A  133 ASP cc_start: 0.8693 (m-30) cc_final: 0.8068 (m-30)
REVERT: A  136 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8341 (mp0)
REVERT: A  139 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7868 (tp-100)
REVERT: A  152 MET cc_start: 0.7267 (mmm) cc_final: 0.7012 (mmm)
REVERT: A  198 GLN cc_start: 0.8493 (mt0) cc_final: 0.7955 (mt0)
REVERT: A  211 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8135 (mtp85)
REVERT: A  213 HIS cc_start: 0.7558 (m90) cc_final: 0.7295 (m-70)
REVERT: A  223 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8184 (mm-40)
REVERT: A  230 TYR cc_start: 0.9176 (m-80) cc_final: 0.8712 (m-80)
REVERT: A  236 ILE cc_start: 0.9337 (mt) cc_final: 0.8761 (tp)
REVERT: A  237 VAL cc_start: 0.9016 (m) cc_final: 0.8319 (p)
REVERT: A  239 ASP cc_start: 0.8758 (m-30) cc_final: 0.8086 (m-30)
REVERT: B  115 LYS cc_start: 0.7436 (ttmp) cc_final: 0.6888 (tptp)
REVERT: B  120 LEU cc_start: 0.8803 (mt) cc_final: 0.8557 (mm)
REVERT: B  124 GLN cc_start: 0.8171 (mp10) cc_final: 0.7871 (tm-30)
REVERT: B  126 TYR cc_start: 0.7156 (m-80) cc_final: 0.6953 (m-80)
REVERT: B  127 LYS cc_start: 0.8902 (ptmt) cc_final: 0.8691 (ptmt)
REVERT: B  136 GLU cc_start: 0.8707 (mp0) cc_final: 0.8290 (mp0)
REVERT: B  204 PHE cc_start: 0.8232 (m-80) cc_final: 0.7895 (m-10)
REVERT: B  236 ILE cc_start: 0.9305 (mt) cc_final: 0.9013 (tp)
REVERT: B  237 VAL cc_start: 0.9067 (m) cc_final: 0.8567 (p)
REVERT: B  239 ASP cc_start: 0.8844 (m-30) cc_final: 0.8438 (m-30)
  outliers start: 27
  outliers final: 18
  residues processed: 127
  average time/residue: 0.0797
  time to fit residues: 11.4001
Evaluate side-chains
  129 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  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  106 PHE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 9 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:   40.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 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 = 0.3645 r_free = 0.3645 target = 0.107222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.085558 restraints weight = 7211.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.088222 restraints weight = 4045.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.089952 restraints weight = 2801.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.091113 restraints weight = 2212.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.091761 restraints weight = 1894.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.6123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   2582  Z= 0.266
  Angle     :  0.845   6.768   3498  Z= 0.447
  Chirality :  0.056   0.214    388
  Planarity :  0.005   0.030    440
  Dihedral  :  6.384  23.310    336
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 25.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers : 10.42 %
    Allowed  : 23.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.48), residues: 302
  helix:  1.04 (0.62), residues: 74
  sheet: -2.26 (0.50), residues: 94
  loop : -2.83 (0.50), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 211 
 TYR   0.019   0.002   TYR B 126 
 PHE   0.021   0.002   PHE A 106 
 TRP   0.006   0.001   TRP A 192 
 HIS   0.015   0.004   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 ( 2580)
  covalent geometry    : angle       0.84412 ( 3494)
  SS BOND              : bond        0.00100 (    2)
  SS BOND              : angle       1.28915 (    4)
  hydrogen bonds       : bond        0.04049 (   94)
  hydrogen bonds       : angle       6.04359 (  300)

*********************** 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
  142 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9078 (pp30) cc_final: 0.8387 (pm20)
REVERT: A  115 LYS cc_start: 0.7835 (tptm) cc_final: 0.7350 (mttm)
REVERT: A  121 MET cc_start: 0.6410 (tpp) cc_final: 0.6030 (tpp)
REVERT: A  134 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8719 (mtm)
REVERT: A  139 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8496 (tp-100)
REVERT: A  198 GLN cc_start: 0.8502 (mt0) cc_final: 0.7632 (pp30)
REVERT: A  211 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.8171 (mtp85)
REVERT: A  213 HIS cc_start: 0.7638 (m90) cc_final: 0.7325 (m-70)
REVERT: A  236 ILE cc_start: 0.9391 (mt) cc_final: 0.8953 (tp)
REVERT: A  237 VAL cc_start: 0.9020 (m) cc_final: 0.8259 (p)
REVERT: A  239 ASP cc_start: 0.8859 (m-30) cc_final: 0.8232 (m-30)
REVERT: B  115 LYS cc_start: 0.7618 (ttmp) cc_final: 0.6932 (tptp)
REVERT: B  120 LEU cc_start: 0.8734 (mt) cc_final: 0.8476 (mm)
REVERT: B  124 GLN cc_start: 0.8159 (mp10) cc_final: 0.7795 (tm-30)
REVERT: B  126 TYR cc_start: 0.7009 (m-10) cc_final: 0.6795 (m-80)
REVERT: B  127 LYS cc_start: 0.8924 (ptmt) cc_final: 0.8527 (ptmt)
REVERT: B  136 GLU cc_start: 0.8751 (mp0) cc_final: 0.8444 (mp0)
REVERT: B  236 ILE cc_start: 0.9445 (mt) cc_final: 0.9083 (tp)
REVERT: B  239 ASP cc_start: 0.8913 (m-30) cc_final: 0.8598 (m-30)
  outliers start: 30
  outliers final: 20
  residues processed: 126
  average time/residue: 0.0855
  time to fit residues: 12.1067
Evaluate side-chains
  130 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  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  184 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 11 optimal weight:   20.0000
   chunk 2 optimal weight:   30.0000
   chunk 15 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9980
   overall best weight:    5.3988

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.106993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.086039 restraints weight = 7254.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.088712 restraints weight = 3982.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.090481 restraints weight = 2721.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.091615 restraints weight = 2130.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.092373 restraints weight = 1820.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.6422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   2582  Z= 0.257
  Angle     :  0.889   6.731   3498  Z= 0.464
  Chirality :  0.058   0.220    388
  Planarity :  0.005   0.031    440
  Dihedral  :  6.510  24.172    336
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 25.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers : 10.42 %
    Allowed  : 24.31 %
    Favored  : 65.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.48), residues: 302
  helix:  0.86 (0.60), residues: 74
  sheet: -2.07 (0.52), residues: 90
  loop : -2.94 (0.50), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 211 
 TYR   0.014   0.002   TYR B 230 
 PHE   0.022   0.002   PHE B 106 
 TRP   0.007   0.001   TRP A 192 
 HIS   0.014   0.004   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00579 ( 2580)
  covalent geometry    : angle       0.88784 ( 3494)
  SS BOND              : bond        0.00033 (    2)
  SS BOND              : angle       1.35082 (    4)
  hydrogen bonds       : bond        0.03892 (   94)
  hydrogen bonds       : angle       6.31261 (  300)

*********************** 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
  143 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8921 (pp30) cc_final: 0.8328 (pm20)
REVERT: A  115 LYS cc_start: 0.7911 (tptm) cc_final: 0.7390 (mttm)
REVERT: A  133 ASP cc_start: 0.8822 (m-30) cc_final: 0.8286 (m-30)
REVERT: A  136 GLU cc_start: 0.8765 (mp0) cc_final: 0.8424 (mp0)
REVERT: A  139 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8422 (tp-100)
REVERT: A  145 MET cc_start: 0.8453 (ttm) cc_final: 0.8099 (ttm)
REVERT: A  152 MET cc_start: 0.7552 (mmm) cc_final: 0.7340 (mmm)
REVERT: A  211 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8261 (mtp85)
REVERT: A  213 HIS cc_start: 0.7621 (m90) cc_final: 0.7352 (m-70)
REVERT: A  236 ILE cc_start: 0.9396 (mt) cc_final: 0.8899 (tp)
REVERT: A  239 ASP cc_start: 0.8876 (m-30) cc_final: 0.8540 (m-30)
REVERT: B  120 LEU cc_start: 0.8710 (mt) cc_final: 0.8413 (mm)
REVERT: B  124 GLN cc_start: 0.8117 (mp10) cc_final: 0.7743 (tm-30)
REVERT: B  127 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8522 (ptmt)
REVERT: B  136 GLU cc_start: 0.8709 (mp0) cc_final: 0.8405 (mp0)
REVERT: B  139 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8500 (tp-100)
REVERT: B  170 ARG cc_start: 0.9162 (tpp-160) cc_final: 0.8839 (tpp80)
REVERT: B  195 GLU cc_start: 0.6954 (tt0) cc_final: 0.6471 (tt0)
REVERT: B  202 GLU cc_start: 0.8072 (tp30) cc_final: 0.7676 (tp30)
REVERT: B  223 GLN cc_start: 0.8380 (mm110) cc_final: 0.7947 (mm-40)
REVERT: B  226 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8832 (mmmt)
REVERT: B  236 ILE cc_start: 0.9454 (mt) cc_final: 0.9134 (tp)
REVERT: B  239 ASP cc_start: 0.8823 (m-30) cc_final: 0.8539 (m-30)
  outliers start: 30
  outliers final: 23
  residues processed: 125
  average time/residue: 0.0848
  time to fit residues: 11.8372
Evaluate side-chains
  136 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  120 LEU
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  184 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  118 GLN
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  169 MET
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0050
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    2.4002

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 197 GLN
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.110198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.088945 restraints weight = 7116.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.091644 restraints weight = 3948.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.093377 restraints weight = 2716.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.094538 restraints weight = 2149.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.095255 restraints weight = 1842.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.6788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   2582  Z= 0.163
  Angle     :  0.873  11.797   3498  Z= 0.438
  Chirality :  0.055   0.209    388
  Planarity :  0.005   0.033    440
  Dihedral  :  6.197  24.111    336
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 21.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.93 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  7.99 %
    Allowed  : 25.35 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.49), residues: 302
  helix:  0.93 (0.62), residues: 72
  sheet: -1.82 (0.54), residues: 90
  loop : -2.93 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 177 
 TYR   0.029   0.002   TYR B 126 
 PHE   0.018   0.002   PHE B 106 
 TRP   0.003   0.001   TRP A 192 
 HIS   0.013   0.003   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 2580)
  covalent geometry    : angle       0.87183 ( 3494)
  SS BOND              : bond        0.00080 (    2)
  SS BOND              : angle       1.47693 (    4)
  hydrogen bonds       : bond        0.03769 (   94)
  hydrogen bonds       : angle       6.49218 (  300)

*********************** 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
  142 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7862 (tptm) cc_final: 0.7398 (mttm)
REVERT: A  136 GLU cc_start: 0.8732 (mp0) cc_final: 0.8268 (mp0)
REVERT: A  139 GLN cc_start: 0.8503 (tp-100) cc_final: 0.8199 (tp-100)
REVERT: A  193 LYS cc_start: 0.7446 (mmtm) cc_final: 0.6943 (mmtp)
REVERT: A  195 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7397 (tt0)
REVERT: A  211 ARG cc_start: 0.8448 (mmm-85) cc_final: 0.8035 (mmp80)
REVERT: A  213 HIS cc_start: 0.7399 (m90) cc_final: 0.7131 (m-70)
REVERT: A  230 TYR cc_start: 0.9209 (m-10) cc_final: 0.8820 (m-80)
REVERT: A  236 ILE cc_start: 0.9288 (mt) cc_final: 0.8812 (tp)
REVERT: A  239 ASP cc_start: 0.8766 (m-30) cc_final: 0.8532 (m-30)
REVERT: B  116 LYS cc_start: 0.6855 (pmtt) cc_final: 0.6280 (ptmm)
REVERT: B  127 LYS cc_start: 0.8652 (ptmt) cc_final: 0.8414 (ptmt)
REVERT: B  135 PRO cc_start: 0.9550 (Cg_endo) cc_final: 0.9066 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8736 (mp0) cc_final: 0.8349 (mp0)
REVERT: B  170 ARG cc_start: 0.9143 (tpp-160) cc_final: 0.8928 (mmt90)
REVERT: B  195 GLU cc_start: 0.7523 (tt0) cc_final: 0.7018 (tt0)
REVERT: B  202 GLU cc_start: 0.7893 (tp30) cc_final: 0.7438 (tp30)
REVERT: B  204 PHE cc_start: 0.8053 (m-80) cc_final: 0.7574 (m-10)
REVERT: B  223 GLN cc_start: 0.8383 (mm110) cc_final: 0.7911 (mm-40)
REVERT: B  226 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8802 (mmmt)
REVERT: B  236 ILE cc_start: 0.9325 (mt) cc_final: 0.8944 (tp)
REVERT: B  237 VAL cc_start: 0.9036 (m) cc_final: 0.8195 (p)
REVERT: B  239 ASP cc_start: 0.8829 (m-30) cc_final: 0.8322 (m-30)
  outliers start: 23
  outliers final: 17
  residues processed: 127
  average time/residue: 0.0926
  time to fit residues: 13.1955
Evaluate side-chains
  133 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
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  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  129 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:   30.0000
   chunk 7 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 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 = 0.3665 r_free = 0.3665 target = 0.108912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.087076 restraints weight = 7281.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.089802 restraints weight = 4028.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.091600 restraints weight = 2786.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.092761 restraints weight = 2204.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.093504 restraints weight = 1894.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.7044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   2582  Z= 0.192
  Angle     :  0.912  11.407   3498  Z= 0.461
  Chirality :  0.055   0.211    388
  Planarity :  0.005   0.035    440
  Dihedral  :  6.291  24.055    336
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 25.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  9.03 %
    Allowed  : 28.12 %
    Favored  : 62.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.49), residues: 302
  helix:  0.86 (0.63), residues: 72
  sheet: -1.94 (0.54), residues: 92
  loop : -2.86 (0.50), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 177 
 TYR   0.009   0.002   TYR A 230 
 PHE   0.018   0.002   PHE B 106 
 TRP   0.004   0.001   TRP A 192 
 HIS   0.012   0.003   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 2580)
  covalent geometry    : angle       0.91132 ( 3494)
  SS BOND              : bond        0.00061 (    2)
  SS BOND              : angle       1.44719 (    4)
  hydrogen bonds       : bond        0.04003 (   94)
  hydrogen bonds       : angle       6.53001 (  300)

*********************** 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
  143 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7914 (tptm) cc_final: 0.7432 (mttm)
REVERT: A  136 GLU cc_start: 0.8801 (mp0) cc_final: 0.8259 (mp0)
REVERT: A  139 GLN cc_start: 0.8795 (tp-100) cc_final: 0.8437 (tp-100)
REVERT: A  195 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7364 (tt0)
REVERT: A  211 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.7920 (mmp80)
REVERT: A  213 HIS cc_start: 0.7470 (m90) cc_final: 0.7195 (m-70)
REVERT: A  236 ILE cc_start: 0.9311 (mt) cc_final: 0.8717 (tp)
REVERT: A  239 ASP cc_start: 0.8844 (m-30) cc_final: 0.8587 (m-30)
REVERT: B  116 LYS cc_start: 0.7003 (pmtt) cc_final: 0.6441 (ptmm)
REVERT: B  135 PRO cc_start: 0.9549 (Cg_endo) cc_final: 0.9139 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8736 (mp0) cc_final: 0.8349 (mp0)
REVERT: B  195 GLU cc_start: 0.7600 (tt0) cc_final: 0.7061 (tt0)
REVERT: B  202 GLU cc_start: 0.7841 (tp30) cc_final: 0.7623 (tp30)
REVERT: B  204 PHE cc_start: 0.8051 (m-80) cc_final: 0.7501 (m-10)
REVERT: B  223 GLN cc_start: 0.8434 (mm110) cc_final: 0.7965 (mm-40)
REVERT: B  236 ILE cc_start: 0.9315 (mt) cc_final: 0.8870 (tp)
REVERT: B  237 VAL cc_start: 0.9009 (m) cc_final: 0.8148 (p)
REVERT: B  239 ASP cc_start: 0.8883 (m-30) cc_final: 0.8420 (m-30)
  outliers start: 26
  outliers final: 20
  residues processed: 126
  average time/residue: 0.0836
  time to fit residues: 11.8979
Evaluate side-chains
  136 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
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  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  129 ILE
Chi-restraints excluded: chain B residue  137 SER
Chi-restraints excluded: chain B residue  145 MET
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3693 r_free = 0.3693 target = 0.110748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.088814 restraints weight = 7282.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.091602 restraints weight = 4071.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.093407 restraints weight = 2828.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.094566 restraints weight = 2243.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.095310 restraints weight = 1932.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.7213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   2582  Z= 0.169
  Angle     :  0.903  10.581   3498  Z= 0.453
  Chirality :  0.056   0.206    388
  Planarity :  0.005   0.035    440
  Dihedral  :  6.248  24.005    336
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 23.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 28.12 %
    Favored  : 64.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.33 (0.50), residues: 302
  helix:  0.79 (0.66), residues: 72
  sheet: -1.76 (0.54), residues: 92
  loop : -2.69 (0.53), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 177 
 TYR   0.012   0.002   TYR B 126 
 PHE   0.017   0.002   PHE B 106 
 TRP   0.003   0.001   TRP A 192 
 HIS   0.013   0.003   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 2580)
  covalent geometry    : angle       0.90243 ( 3494)
  SS BOND              : bond        0.00078 (    2)
  SS BOND              : angle       1.43542 (    4)
  hydrogen bonds       : bond        0.03858 (   94)
  hydrogen bonds       : angle       6.43122 (  300)

*********************** 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
  139 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7874 (tptm) cc_final: 0.7426 (mttm)
REVERT: A  136 GLU cc_start: 0.8775 (mp0) cc_final: 0.8316 (mp0)
REVERT: A  139 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8331 (tp-100)
REVERT: A  193 LYS cc_start: 0.7234 (mmtm) cc_final: 0.6812 (mmtp)
REVERT: A  195 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7489 (tt0)
REVERT: A  211 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.7899 (mmp80)
REVERT: A  213 HIS cc_start: 0.7367 (m90) cc_final: 0.7093 (m90)
REVERT: A  236 ILE cc_start: 0.9273 (mt) cc_final: 0.8685 (tp)
REVERT: A  239 ASP cc_start: 0.8810 (m-30) cc_final: 0.8567 (m-30)
REVERT: B  116 LYS cc_start: 0.6948 (pmtt) cc_final: 0.6457 (ptmm)
REVERT: B  135 PRO cc_start: 0.9515 (Cg_endo) cc_final: 0.8996 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8633 (mp0) cc_final: 0.8338 (mp0)
REVERT: B  170 ARG cc_start: 0.9184 (tpp-160) cc_final: 0.8805 (tpp80)
REVERT: B  195 GLU cc_start: 0.7668 (tt0) cc_final: 0.7283 (tt0)
REVERT: B  204 PHE cc_start: 0.7849 (m-80) cc_final: 0.7609 (m-10)
REVERT: B  225 GLN cc_start: 0.8778 (pm20) cc_final: 0.8542 (pm20)
REVERT: B  226 LYS cc_start: 0.9334 (mmmm) cc_final: 0.8769 (mmmt)
REVERT: B  236 ILE cc_start: 0.9236 (mt) cc_final: 0.8812 (tp)
REVERT: B  237 VAL cc_start: 0.8896 (m) cc_final: 0.8014 (p)
REVERT: B  239 ASP cc_start: 0.8751 (m-30) cc_final: 0.8156 (m-30)
REVERT: B  240 PHE cc_start: 0.4790 (p90) cc_final: 0.3844 (m-80)
  outliers start: 22
  outliers final: 21
  residues processed: 127
  average time/residue: 0.0890
  time to fit residues: 12.7073
Evaluate side-chains
  137 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
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  130 VAL
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  129 ILE
Chi-restraints excluded: chain B residue  137 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  93 GLN
A 235 HIS
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.115108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.093208 restraints weight = 7067.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.095967 restraints weight = 3870.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.097767 restraints weight = 2656.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.098900 restraints weight = 2089.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.099306 restraints weight = 1803.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.7553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   2582  Z= 0.154
  Angle     :  0.920  10.356   3498  Z= 0.454
  Chirality :  0.056   0.210    388
  Planarity :  0.005   0.039    440
  Dihedral  :  6.127  24.094    336
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 21.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.93 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 31.25 %
    Favored  : 63.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.50), residues: 302
  helix:  0.69 (0.64), residues: 72
  sheet: -1.48 (0.56), residues: 92
  loop : -2.58 (0.53), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 177 
 TYR   0.013   0.001   TYR B 126 
 PHE   0.015   0.001   PHE B 106 
 TRP   0.003   0.000   TRP A 182 
 HIS   0.012   0.002   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 2580)
  covalent geometry    : angle       0.91914 ( 3494)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       1.46209 (    4)
  hydrogen bonds       : bond        0.03751 (   94)
  hydrogen bonds       : angle       6.58735 (  300)

********************** 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
  141 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.8632 (mp0) cc_final: 0.7406 (mp0)
REVERT: A  139 GLN cc_start: 0.8338 (tp-100) cc_final: 0.7904 (tp-100)
REVERT: A  152 MET cc_start: 0.6798 (mmm) cc_final: 0.6335 (mmm)
REVERT: A  193 LYS cc_start: 0.7215 (mmtm) cc_final: 0.6751 (mmtp)
REVERT: A  195 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7722 (tt0)
REVERT: A  211 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7990 (mmp80)
REVERT: A  213 HIS cc_start: 0.7249 (m90) cc_final: 0.7007 (m90)
REVERT: A  236 ILE cc_start: 0.9187 (mt) cc_final: 0.8640 (tp)
REVERT: A  239 ASP cc_start: 0.8808 (m-30) cc_final: 0.8569 (m-30)
REVERT: B  116 LYS cc_start: 0.7136 (pmtt) cc_final: 0.6738 (ptmm)
REVERT: B  135 PRO cc_start: 0.9314 (Cg_endo) cc_final: 0.8759 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8628 (mp0) cc_final: 0.8360 (mp0)
REVERT: B  170 ARG cc_start: 0.9158 (tpp-160) cc_final: 0.8957 (mmt90)
REVERT: B  195 GLU cc_start: 0.7557 (tt0) cc_final: 0.7211 (tt0)
REVERT: B  226 LYS cc_start: 0.9353 (mmmm) cc_final: 0.8940 (mmmt)
REVERT: B  236 ILE cc_start: 0.9158 (mt) cc_final: 0.8755 (tp)
REVERT: B  237 VAL cc_start: 0.8784 (m) cc_final: 0.7999 (p)
REVERT: B  239 ASP cc_start: 0.8343 (m-30) cc_final: 0.7762 (m-30)
REVERT: B  240 PHE cc_start: 0.4545 (p90) cc_final: 0.3647 (m-80)
  outliers start: 16
  outliers final: 15
  residues processed: 132
  average time/residue: 0.0777
  time to fit residues: 11.6274
Evaluate side-chains
  132 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
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  130 VAL
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  137 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 11 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 235 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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.115099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.093718 restraints weight = 7038.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.096463 restraints weight = 3947.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.098133 restraints weight = 2694.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.099394 restraints weight = 2119.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.100189 restraints weight = 1795.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.7703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.357   2582  Z= 0.491
  Angle     :  1.725  59.194   3498  Z= 0.959
  Chirality :  0.063   0.364    388
  Planarity :  0.007   0.039    440
  Dihedral  :  6.244  24.025    336
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 31.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 31.94 %
    Favored  : 62.50 %
  Cbeta Deviations :  0.34 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.50), residues: 302
  helix:  0.63 (0.63), residues: 72
  sheet: -1.51 (0.56), residues: 92
  loop : -2.62 (0.53), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 177 
 TYR   0.013   0.001   TYR B 126 
 PHE   0.024   0.003   PHE B 204 
 TRP   0.003   0.001   TRP A 182 
 HIS   0.013   0.003   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.01307 ( 2580)
  covalent geometry    : angle       1.72498 ( 3494)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       1.44756 (    4)
  hydrogen bonds       : bond        0.03749 (   94)
  hydrogen bonds       : angle       6.67644 (  300)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 663.68 seconds
wall clock time: 12 minutes 5.15 seconds (725.15 seconds total)