Starting phenix.real_space_refine
on Sat Apr 26 16:53:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6mlu_9146/04_2025/6mlu_9146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6mlu_9146/04_2025/6mlu_9146.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6mlu_9146/04_2025/6mlu_9146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6mlu_9146/04_2025/6mlu_9146.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6mlu_9146/04_2025/6mlu_9146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6mlu_9146/04_2025/6mlu_9146.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    1616      2.51       5
     N     426      2.21       5
     O     446      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 2516
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1258
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 9, 'TRANS': 143}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.51, per 1000 atoms: 1.00
  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: 0.58
  Conformation dependent library (CDL) restraints added in 294.9 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: 0.30
  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: 0.64

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 796
        1.34 -     1.46: 577
        1.46 -     1.58: 1159
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 2580
  Sorted by residual:
  bond pdb=" CA  HIS A 110 "
       pdb=" CB  HIS A 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.564 -0.033 1.69e-02 3.50e+03 3.91e+00
  bond pdb=" CA  HIS B 110 "
       pdb=" CB  HIS B 110 "
    ideal  model  delta    sigma   weight residual
    1.530  1.564 -0.033 1.69e-02 3.50e+03 3.89e+00
  bond pdb=" CA  ARG A  88 "
       pdb=" C   ARG A  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.555 -0.030 2.10e-02 2.27e+03 2.02e+00
  bond pdb=" CA  ARG B  88 "
       pdb=" C   ARG B  88 "
    ideal  model  delta    sigma   weight residual
    1.525  1.554 -0.029 2.10e-02 2.27e+03 1.88e+00
  bond pdb=" N   HIS B 110 "
       pdb=" CA  HIS B 110 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.45e+00
  ... (remaining 2575 not shown)

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

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.37: 1401
       11.37 -    22.73: 135
       22.73 -    34.09: 24
       34.09 -    45.46: 12
       45.46 -    56.82: 6
  Dihedral angle restraints: 1578
    sinusoidal: 664
      harmonic: 914
  Sorted by residual:
  dihedral pdb=" CA  HIS B 110 "
           pdb=" C   HIS B 110 "
           pdb=" N   VAL B 111 "
           pdb=" CA  VAL B 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.73   23.27     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  HIS A 110 "
           pdb=" C   HIS A 110 "
           pdb=" N   VAL A 111 "
           pdb=" CA  VAL A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.82   23.18     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  TRP A 192 "
           pdb=" C   TRP A 192 "
           pdb=" N   LYS A 193 "
           pdb=" CA  LYS A 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.35   22.65     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 1575 not shown)

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

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

  Histogram of nonbonded interaction distances:
        2.41 -     2.90: 921
        2.90 -     3.40: 2472
        3.40 -     3.90: 4091
        3.90 -     4.40: 4488
        4.40 -     4.90: 7629
  Nonbonded interactions: 19601
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 154 "
            pdb=" N   MET A 158 "
     model   vdw
     2.406 3.120
  nonbonded pdb=" OD1 ASP B 154 "
            pdb=" N   MET B 158 "
     model   vdw
     2.409 3.120
  nonbonded pdb=" NH1 ARG B 206 "
            pdb=" O   PHE B 240 "
     model   vdw
     2.415 3.120
  nonbonded pdb=" NH1 ARG A 206 "
            pdb=" O   PHE A 240 "
     model   vdw
     2.415 3.120
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" N   TYR B 171 "
     model   vdw
     2.432 3.120
  ... (remaining 19596 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.790
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.38 (0.42), residues: 302
  helix: -2.79 (0.45), residues: 74
  sheet: -1.76 (0.57), residues: 86
  loop : -3.75 (0.42), residues: 142

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

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

*********************** 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  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.8839 (m-30) cc_final: 0.8375 (m-30)
REVERT: A  137 SER cc_start: 0.9203 (t) cc_final: 0.8998 (p)
REVERT: A  147 MET cc_start: 0.8306 (mmm) cc_final: 0.7641 (tpp)
REVERT: A  165 ARG cc_start: 0.7552 (mmt-90) cc_final: 0.7122 (mmt180)
REVERT: A  177 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7831 (mtm-85)
REVERT: A  195 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7635 (mt-10)
REVERT: A  197 GLN cc_start: 0.8825 (mt0) cc_final: 0.8597 (mp-120)
REVERT: A  198 GLN cc_start: 0.8748 (mt0) cc_final: 0.8529 (mt0)
REVERT: A  202 GLU cc_start: 0.8764 (tt0) cc_final: 0.8201 (tm-30)
REVERT: A  204 PHE cc_start: 0.8056 (m-80) cc_final: 0.7746 (m-80)
REVERT: A  223 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8401 (mm-40)
REVERT: A  232 VAL cc_start: 0.9659 (t) cc_final: 0.8480 (t)
REVERT: A  236 ILE cc_start: 0.9238 (mt) cc_final: 0.8963 (tp)
REVERT: A  237 VAL cc_start: 0.8740 (m) cc_final: 0.8274 (p)
REVERT: A  239 ASP cc_start: 0.8777 (m-30) cc_final: 0.8247 (m-30)
REVERT: B  115 LYS cc_start: 0.6956 (ttmp) cc_final: 0.6727 (tptm)
REVERT: B  133 ASP cc_start: 0.8724 (m-30) cc_final: 0.8410 (m-30)
REVERT: B  177 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.8038 (mtm-85)
REVERT: B  202 GLU cc_start: 0.8888 (tt0) cc_final: 0.8301 (tm-30)
REVERT: B  232 VAL cc_start: 0.9717 (t) cc_final: 0.8700 (t)
REVERT: B  236 ILE cc_start: 0.9343 (mt) cc_final: 0.9043 (tp)
REVERT: B  237 VAL cc_start: 0.8879 (m) cc_final: 0.8238 (p)
REVERT: B  239 ASP cc_start: 0.8877 (m-30) cc_final: 0.8536 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2186
  time to fit residues: 39.4010
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  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    2.3188

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

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

Total number of N/Q/H flips: 3

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2582  Z= 0.179
  Angle     :  0.819   7.403   3498  Z= 0.429
  Chirality :  0.054   0.203    388
  Planarity :  0.006   0.030    440
  Dihedral  :  6.264  23.418    336
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 16.32 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.32 (0.46), residues: 302
  helix: -0.63 (0.57), residues: 74
  sheet: -1.83 (0.52), residues: 90
  loop : -3.40 (0.48), residues: 138

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05346 (   94)
  hydrogen bonds       : angle       6.05865 (  300)
  SS BOND              : bond        0.00022 (    2)
  SS BOND              : angle       1.52816 (    4)
  covalent geometry    : bond        0.00377 ( 2580)
  covalent geometry    : angle       0.81820 ( 3494)

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

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8755 (pm20) cc_final: 0.8433 (pm20)
REVERT: A   95 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7967 (tppt)
REVERT: A   99 GLU cc_start: 0.8148 (pm20) cc_final: 0.7648 (pm20)
REVERT: A  116 LYS cc_start: 0.7754 (pmtt) cc_final: 0.7548 (ptmt)
REVERT: A  120 LEU cc_start: 0.8696 (mt) cc_final: 0.8337 (mt)
REVERT: A  124 GLN cc_start: 0.7128 (mp10) cc_final: 0.5781 (tm-30)
REVERT: A  133 ASP cc_start: 0.8691 (m-30) cc_final: 0.8162 (m-30)
REVERT: A  147 MET cc_start: 0.8210 (mmm) cc_final: 0.7505 (tpp)
REVERT: A  165 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7306 (mmt180)
REVERT: A  198 GLN cc_start: 0.8595 (mt0) cc_final: 0.8295 (mt0)
REVERT: A  202 GLU cc_start: 0.8439 (tt0) cc_final: 0.7958 (tm-30)
REVERT: A  204 PHE cc_start: 0.8148 (m-80) cc_final: 0.7469 (m-80)
REVERT: A  213 HIS cc_start: 0.7651 (m90) cc_final: 0.7394 (m-70)
REVERT: A  230 TYR cc_start: 0.9170 (m-80) cc_final: 0.8715 (m-80)
REVERT: A  236 ILE cc_start: 0.9257 (mt) cc_final: 0.9031 (tp)
REVERT: A  237 VAL cc_start: 0.9087 (m) cc_final: 0.8546 (p)
REVERT: A  239 ASP cc_start: 0.8759 (m-30) cc_final: 0.8278 (m-30)
REVERT: B  115 LYS cc_start: 0.7072 (ttmp) cc_final: 0.6679 (tptm)
REVERT: B  120 LEU cc_start: 0.8833 (mt) cc_final: 0.8367 (mm)
REVERT: B  127 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8155 (ptmt)
REVERT: B  133 ASP cc_start: 0.8531 (m-30) cc_final: 0.8293 (m-30)
REVERT: B  152 MET cc_start: 0.7456 (mmm) cc_final: 0.7073 (mmm)
REVERT: B  202 GLU cc_start: 0.8828 (tt0) cc_final: 0.8460 (tm-30)
REVERT: B  204 PHE cc_start: 0.8229 (m-80) cc_final: 0.7877 (m-10)
REVERT: B  211 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.7987 (mmp80)
REVERT: B  223 GLN cc_start: 0.8439 (mm110) cc_final: 0.7797 (mm-40)
REVERT: B  226 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8855 (mmmt)
REVERT: B  236 ILE cc_start: 0.9347 (mt) cc_final: 0.9013 (tp)
REVERT: B  237 VAL cc_start: 0.9087 (m) cc_final: 0.8189 (p)
REVERT: B  239 ASP cc_start: 0.8874 (m-30) cc_final: 0.8071 (p0)
  outliers start: 20
  outliers final: 10
  residues processed: 138
  average time/residue: 0.2022
  time to fit residues: 31.1894
Evaluate side-chains
  130 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  227 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 27 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0470
   chunk 13 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    3.5484

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.108734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.087730 restraints weight = 7268.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.090374 restraints weight = 4108.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.092127 restraints weight = 2852.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.5236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2582  Z= 0.198
  Angle     :  0.795   7.225   3498  Z= 0.416
  Chirality :  0.054   0.222    388
  Planarity :  0.005   0.027    440
  Dihedral  :  6.176  22.712    336
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 21.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers : 10.76 %
    Allowed  : 21.18 %
    Favored  : 68.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.47), residues: 302
  helix:  0.15 (0.59), residues: 74
  sheet: -2.15 (0.51), residues: 94
  loop : -3.12 (0.50), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 192 
 HIS   0.013   0.003   HIS A 110 
 PHE   0.019   0.002   PHE A 106 
 TYR   0.026   0.002   TYR B 126 
 ARG   0.003   0.000   ARG A  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04432 (   94)
  hydrogen bonds       : angle       6.03511 (  300)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       1.52164 (    4)
  covalent geometry    : bond        0.00429 ( 2580)
  covalent geometry    : angle       0.79424 ( 3494)

*********************** 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
  152 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7937 (tppt)
REVERT: A  115 LYS cc_start: 0.7926 (tptm) cc_final: 0.7678 (mttm)
REVERT: A  116 LYS cc_start: 0.7632 (pmtt) cc_final: 0.7201 (tmtt)
REVERT: A  121 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6109 (tpp)
REVERT: A  133 ASP cc_start: 0.8674 (m-30) cc_final: 0.8091 (m-30)
REVERT: A  136 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8311 (mp0)
REVERT: A  152 MET cc_start: 0.7132 (mmm) cc_final: 0.6814 (mmm)
REVERT: A  198 GLN cc_start: 0.8524 (mt0) cc_final: 0.8071 (mt0)
REVERT: A  204 PHE cc_start: 0.8190 (m-80) cc_final: 0.7712 (m-80)
REVERT: A  213 HIS cc_start: 0.7782 (m90) cc_final: 0.7513 (m-70)
REVERT: A  223 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8202 (mm-40)
REVERT: A  230 TYR cc_start: 0.9166 (m-80) cc_final: 0.8619 (m-80)
REVERT: A  236 ILE cc_start: 0.9290 (mt) cc_final: 0.8971 (tp)
REVERT: A  237 VAL cc_start: 0.9104 (m) cc_final: 0.8546 (p)
REVERT: A  239 ASP cc_start: 0.8740 (m-30) cc_final: 0.8304 (m-30)
REVERT: B  115 LYS cc_start: 0.7262 (ttmp) cc_final: 0.6790 (tptp)
REVERT: B  121 MET cc_start: 0.6529 (tmm) cc_final: 0.6329 (tpp)
REVERT: B  124 GLN cc_start: 0.8184 (mp10) cc_final: 0.7944 (tm-30)
REVERT: B  126 TYR cc_start: 0.7415 (m-80) cc_final: 0.7031 (m-80)
REVERT: B  127 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8162 (ptmt)
REVERT: B  136 GLU cc_start: 0.8806 (mp0) cc_final: 0.8507 (mp0)
REVERT: B  139 GLN cc_start: 0.8687 (tp40) cc_final: 0.8481 (tp-100)
REVERT: B  202 GLU cc_start: 0.8682 (tt0) cc_final: 0.8472 (tm-30)
REVERT: B  211 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7887 (mmp80)
REVERT: B  218 VAL cc_start: 0.9377 (m) cc_final: 0.9140 (t)
REVERT: B  236 ILE cc_start: 0.9322 (mt) cc_final: 0.8997 (tp)
REVERT: B  237 VAL cc_start: 0.9109 (m) cc_final: 0.8250 (p)
REVERT: B  239 ASP cc_start: 0.8877 (m-30) cc_final: 0.8016 (p0)
  outliers start: 31
  outliers final: 19
  residues processed: 133
  average time/residue: 0.2160
  time to fit residues: 32.2928
Evaluate side-chains
  133 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  121 MET
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  127 LYS
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   chunk 2 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    2.7788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.110217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.088635 restraints weight = 7294.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.091215 restraints weight = 4131.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.092995 restraints weight = 2870.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.5724

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= 0.169
  Angle     :  0.778   7.018   3498  Z= 0.403
  Chirality :  0.054   0.219    388
  Planarity :  0.005   0.034    440
  Dihedral  :  6.108  23.381    336
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 22.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers : 10.07 %
    Allowed  : 23.26 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.47), residues: 302
  helix:  0.71 (0.60), residues: 72
  sheet: -2.08 (0.51), residues: 94
  loop : -3.10 (0.49), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 192 
 HIS   0.012   0.003   HIS A 110 
 PHE   0.019   0.002   PHE B 106 
 TYR   0.021   0.002   TYR A 126 
 ARG   0.002   0.000   ARG A  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03876 (   94)
  hydrogen bonds       : angle       6.14720 (  300)
  SS BOND              : bond        0.00079 (    2)
  SS BOND              : angle       1.60538 (    4)
  covalent geometry    : bond        0.00372 ( 2580)
  covalent geometry    : angle       0.77624 ( 3494)

*********************** 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
  144 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 LYS cc_start: 0.7790 (tptm) cc_final: 0.7441 (mttm)
REVERT: A  116 LYS cc_start: 0.7822 (pmtt) cc_final: 0.7575 (ptmm)
REVERT: A  121 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6227 (tpt)
REVERT: A  133 ASP cc_start: 0.8687 (m-30) cc_final: 0.7977 (m-30)
REVERT: A  136 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8312 (mp0)
REVERT: A  139 GLN cc_start: 0.8230 (tp-100) cc_final: 0.8009 (tp40)
REVERT: A  152 MET cc_start: 0.7241 (mmm) cc_final: 0.6965 (mmm)
REVERT: A  198 GLN cc_start: 0.8471 (mt0) cc_final: 0.7895 (mt0)
REVERT: A  213 HIS cc_start: 0.7578 (m90) cc_final: 0.7306 (m-70)
REVERT: A  221 GLU cc_start: 0.8070 (pt0) cc_final: 0.7863 (tm-30)
REVERT: A  230 TYR cc_start: 0.9158 (m-80) cc_final: 0.8787 (m-80)
REVERT: A  236 ILE cc_start: 0.9277 (mt) cc_final: 0.8830 (tp)
REVERT: A  237 VAL cc_start: 0.9025 (m) cc_final: 0.8344 (p)
REVERT: A  239 ASP cc_start: 0.8795 (m-30) cc_final: 0.8141 (m-30)
REVERT: B  115 LYS cc_start: 0.7289 (ttmp) cc_final: 0.6720 (tptp)
REVERT: B  120 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8308 (mm)
REVERT: B  124 GLN cc_start: 0.8243 (mp10) cc_final: 0.7964 (tm-30)
REVERT: B  126 TYR cc_start: 0.7186 (m-80) cc_final: 0.6690 (m-80)
REVERT: B  136 GLU cc_start: 0.8693 (mp0) cc_final: 0.8190 (mp0)
REVERT: B  147 MET cc_start: 0.8913 (tpp) cc_final: 0.8701 (tpp)
REVERT: B  204 PHE cc_start: 0.8493 (m-80) cc_final: 0.7921 (m-10)
REVERT: B  223 GLN cc_start: 0.8373 (mm110) cc_final: 0.7864 (mm-40)
REVERT: B  236 ILE cc_start: 0.9290 (mt) cc_final: 0.8990 (tp)
REVERT: B  237 VAL cc_start: 0.9078 (m) cc_final: 0.8560 (p)
REVERT: B  239 ASP cc_start: 0.8858 (m-30) cc_final: 0.8436 (m-30)
  outliers start: 29
  outliers final: 18
  residues processed: 126
  average time/residue: 0.2043
  time to fit residues: 28.8383
Evaluate side-chains
  132 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 MET
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    3.7588

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.108945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.086707 restraints weight = 7466.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.089502 restraints weight = 4296.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.091343 restraints weight = 3022.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.6066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2582  Z= 0.196
  Angle     :  0.798   6.910   3498  Z= 0.417
  Chirality :  0.055   0.203    388
  Planarity :  0.005   0.032    440
  Dihedral  :  6.159  21.491    336
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 23.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers : 12.50 %
    Allowed  : 23.96 %
    Favored  : 63.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.48), residues: 302
  helix:  0.95 (0.61), residues: 72
  sheet: -1.98 (0.52), residues: 94
  loop : -3.02 (0.49), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 192 
 HIS   0.014   0.003   HIS B 110 
 PHE   0.018   0.002   PHE A 106 
 TYR   0.016   0.002   TYR B 126 
 ARG   0.004   0.001   ARG B 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03829 (   94)
  hydrogen bonds       : angle       6.26713 (  300)
  SS BOND              : bond        0.00043 (    2)
  SS BOND              : angle       1.44667 (    4)
  covalent geometry    : bond        0.00445 ( 2580)
  covalent geometry    : angle       0.79666 ( 3494)

*********************** 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
  149 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 113
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8113 (tppt)
REVERT: A  115 LYS cc_start: 0.7880 (tptm) cc_final: 0.7464 (mttm)
REVERT: A  116 LYS cc_start: 0.7749 (pmtt) cc_final: 0.7533 (ptmm)
REVERT: A  121 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5982 (tpt)
REVERT: A  136 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8442 (mp0)
REVERT: A  139 GLN cc_start: 0.8394 (tp-100) cc_final: 0.8000 (tp-100)
REVERT: A  198 GLN cc_start: 0.8461 (mt0) cc_final: 0.7657 (pp30)
REVERT: A  211 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.8213 (mtp85)
REVERT: A  213 HIS cc_start: 0.7569 (m90) cc_final: 0.7302 (m-70)
REVERT: A  230 TYR cc_start: 0.9229 (m-80) cc_final: 0.8734 (m-80)
REVERT: A  236 ILE cc_start: 0.9249 (mt) cc_final: 0.8824 (tp)
REVERT: A  237 VAL cc_start: 0.9033 (m) cc_final: 0.8344 (p)
REVERT: A  239 ASP cc_start: 0.8865 (m-30) cc_final: 0.8254 (m-30)
REVERT: B  115 LYS cc_start: 0.7599 (ttmp) cc_final: 0.6899 (tptp)
REVERT: B  120 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8401 (mp)
REVERT: B  124 GLN cc_start: 0.8343 (mp10) cc_final: 0.8022 (tm-30)
REVERT: B  126 TYR cc_start: 0.6787 (m-10) cc_final: 0.6531 (m-80)
REVERT: B  136 GLU cc_start: 0.8723 (mp0) cc_final: 0.8349 (mp0)
REVERT: B  211 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7518 (mmp80)
REVERT: B  226 LYS cc_start: 0.9328 (mmmm) cc_final: 0.9002 (mmmt)
REVERT: B  236 ILE cc_start: 0.9320 (mt) cc_final: 0.8919 (tp)
REVERT: B  237 VAL cc_start: 0.9066 (m) cc_final: 0.8090 (p)
REVERT: B  239 ASP cc_start: 0.8904 (m-30) cc_final: 0.7807 (p0)
  outliers start: 36
  outliers final: 18
  residues processed: 129
  average time/residue: 0.2002
  time to fit residues: 28.9689
Evaluate side-chains
  132 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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  106 PHE
Chi-restraints excluded: chain A residue  121 MET
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  156 ASP
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  120 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 23 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0270
   chunk 7 optimal weight:    8.9990
   chunk 28 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    2.0242

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.110168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.089322 restraints weight = 7194.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.092089 restraints weight = 3849.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.093898 restraints weight = 2603.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.6374

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= 0.155
  Angle     :  0.807   7.523   3498  Z= 0.414
  Chirality :  0.055   0.223    388
  Planarity :  0.005   0.032    440
  Dihedral  :  6.071  23.603    336
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 22.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.93 %
    Favored  : 89.07 %
  Rotamer:
    Outliers : 10.42 %
    Allowed  : 26.04 %
    Favored  : 63.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.49), residues: 302
  helix:  1.07 (0.62), residues: 72
  sheet: -1.62 (0.55), residues: 90
  loop : -2.99 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 182 
 HIS   0.012   0.002   HIS B 110 
 PHE   0.016   0.002   PHE B 106 
 TYR   0.014   0.002   TYR B 126 
 ARG   0.003   0.000   ARG A 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03536 (   94)
  hydrogen bonds       : angle       6.33348 (  300)
  SS BOND              : bond        0.00018 (    2)
  SS BOND              : angle       1.50027 (    4)
  covalent geometry    : bond        0.00353 ( 2580)
  covalent geometry    : angle       0.80616 ( 3494)

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

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9100 (pp30) cc_final: 0.8618 (pp30)
REVERT: A   95 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7922 (tppt)
REVERT: A  115 LYS cc_start: 0.7887 (tptm) cc_final: 0.7462 (mttm)
REVERT: A  116 LYS cc_start: 0.7747 (pmtt) cc_final: 0.7417 (tmtt)
REVERT: A  121 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5948 (tpt)
REVERT: A  133 ASP cc_start: 0.8670 (m-30) cc_final: 0.8274 (m-30)
REVERT: A  136 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7359 (mp0)
REVERT: A  139 GLN cc_start: 0.8345 (tp-100) cc_final: 0.8074 (tp40)
REVERT: A  145 MET cc_start: 0.8410 (ttm) cc_final: 0.8150 (ttm)
REVERT: A  211 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8115 (mtp85)
REVERT: A  213 HIS cc_start: 0.7447 (m90) cc_final: 0.7194 (m-70)
REVERT: A  221 GLU cc_start: 0.7737 (pp20) cc_final: 0.6702 (pp20)
REVERT: A  223 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8379 (mm-40)
REVERT: A  230 TYR cc_start: 0.9187 (m-80) cc_final: 0.8596 (m-80)
REVERT: A  232 VAL cc_start: 0.9226 (t) cc_final: 0.8862 (m)
REVERT: A  236 ILE cc_start: 0.9258 (mt) cc_final: 0.8693 (tp)
REVERT: A  239 ASP cc_start: 0.8804 (m-30) cc_final: 0.8535 (m-30)
REVERT: B  116 LYS cc_start: 0.7038 (pmtt) cc_final: 0.6557 (ptmm)
REVERT: B  120 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8442 (mp)
REVERT: B  124 GLN cc_start: 0.8263 (mp10) cc_final: 0.7931 (tm-30)
REVERT: B  126 TYR cc_start: 0.6680 (m-10) cc_final: 0.6343 (m-80)
REVERT: B  135 PRO cc_start: 0.9545 (Cg_endo) cc_final: 0.9198 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8693 (mp0) cc_final: 0.8309 (mp0)
REVERT: B  152 MET cc_start: 0.7693 (mmm) cc_final: 0.7215 (mmm)
REVERT: B  195 GLU cc_start: 0.7357 (tt0) cc_final: 0.6822 (tt0)
REVERT: B  204 PHE cc_start: 0.8199 (m-80) cc_final: 0.7870 (m-10)
REVERT: B  211 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.7971 (mtp85)
REVERT: B  223 GLN cc_start: 0.8559 (mm110) cc_final: 0.8128 (mm-40)
REVERT: B  226 LYS cc_start: 0.9265 (mmmm) cc_final: 0.9044 (mmmt)
REVERT: B  236 ILE cc_start: 0.9175 (mt) cc_final: 0.8863 (tp)
REVERT: B  237 VAL cc_start: 0.9045 (m) cc_final: 0.8496 (p)
REVERT: B  239 ASP cc_start: 0.8909 (m-30) cc_final: 0.8453 (m-30)
  outliers start: 30
  outliers final: 19
  residues processed: 126
  average time/residue: 0.2178
  time to fit residues: 30.7119
Evaluate side-chains
  137 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LYS
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  121 MET
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  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  100 THR
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0770
   chunk 14 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    3.2146

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.110245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.087778 restraints weight = 7418.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.090524 restraints weight = 4279.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.092324 restraints weight = 3019.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.6597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   2582  Z= 0.181
  Angle     :  0.820   6.753   3498  Z= 0.426
  Chirality :  0.055   0.206    388
  Planarity :  0.005   0.036    440
  Dihedral  :  6.057  23.513    336
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 22.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers : 10.42 %
    Allowed  : 23.61 %
    Favored  : 65.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.48), residues: 302
  helix:  1.04 (0.63), residues: 72
  sheet: -1.79 (0.55), residues: 82
  loop : -3.00 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 192 
 HIS   0.013   0.003   HIS B 110 
 PHE   0.017   0.002   PHE B 106 
 TYR   0.013   0.002   TYR B 171 
 ARG   0.003   0.000   ARG A 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (   94)
  hydrogen bonds       : angle       6.29572 (  300)
  SS BOND              : bond        0.00064 (    2)
  SS BOND              : angle       1.43748 (    4)
  covalent geometry    : bond        0.00417 ( 2580)
  covalent geometry    : angle       0.81919 ( 3494)

*********************** 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
  149 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9068 (pp30) cc_final: 0.8544 (pp30)
REVERT: A  115 LYS cc_start: 0.7798 (tptm) cc_final: 0.7223 (mttm)
REVERT: A  116 LYS cc_start: 0.7735 (pmtt) cc_final: 0.7507 (ptmm)
REVERT: A  121 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5966 (tpt)
REVERT: A  139 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7863 (tp-100)
REVERT: A  145 MET cc_start: 0.8383 (ttm) cc_final: 0.8122 (ttm)
REVERT: A  152 MET cc_start: 0.7430 (mmm) cc_final: 0.7205 (mmm)
REVERT: A  193 LYS cc_start: 0.7554 (mmtm) cc_final: 0.7075 (mmtp)
REVERT: A  202 GLU cc_start: 0.7917 (tp30) cc_final: 0.7677 (tp30)
REVERT: A  211 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.8095 (mtp85)
REVERT: A  213 HIS cc_start: 0.7614 (m90) cc_final: 0.7374 (m-70)
REVERT: A  221 GLU cc_start: 0.7889 (pp20) cc_final: 0.7545 (pp20)
REVERT: A  230 TYR cc_start: 0.9148 (m-80) cc_final: 0.8509 (m-80)
REVERT: A  232 VAL cc_start: 0.9166 (t) cc_final: 0.8798 (m)
REVERT: A  236 ILE cc_start: 0.9226 (mt) cc_final: 0.8737 (tp)
REVERT: A  239 ASP cc_start: 0.8851 (m-30) cc_final: 0.8448 (m-30)
REVERT: B  116 LYS cc_start: 0.7089 (pmtt) cc_final: 0.6600 (ptmm)
REVERT: B  120 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8441 (mp)
REVERT: B  124 GLN cc_start: 0.8299 (mp10) cc_final: 0.7961 (tm-30)
REVERT: B  126 TYR cc_start: 0.6313 (m-10) cc_final: 0.6000 (m-80)
REVERT: B  135 PRO cc_start: 0.9524 (Cg_endo) cc_final: 0.9140 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8637 (mp0) cc_final: 0.8389 (mp0)
REVERT: B  152 MET cc_start: 0.7899 (mmm) cc_final: 0.7400 (mmm)
REVERT: B  195 GLU cc_start: 0.7493 (tt0) cc_final: 0.7056 (tt0)
REVERT: B  204 PHE cc_start: 0.8141 (m-80) cc_final: 0.7940 (m-10)
REVERT: B  211 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.8155 (mtp85)
REVERT: B  226 LYS cc_start: 0.9331 (mmmm) cc_final: 0.8992 (mmmt)
REVERT: B  236 ILE cc_start: 0.9179 (mt) cc_final: 0.8853 (tp)
REVERT: B  237 VAL cc_start: 0.9020 (m) cc_final: 0.8455 (p)
REVERT: B  239 ASP cc_start: 0.8989 (m-30) cc_final: 0.8529 (m-30)
  outliers start: 30
  outliers final: 22
  residues processed: 130
  average time/residue: 0.2152
  time to fit residues: 31.3312
Evaluate side-chains
  136 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  121 MET
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  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  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  118 GLN
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    6.9990
   chunk 12 optimal weight:   20.0000
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   overall best weight:    4.3988

-------------------------------------------------------------------------------
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**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 GLN
** B  93 GLN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.108519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.087443 restraints weight = 7194.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.090172 restraints weight = 3919.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.091981 restraints weight = 2678.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.6833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   2582  Z= 0.225
  Angle     :  0.912  11.158   3498  Z= 0.462
  Chirality :  0.058   0.246    388
  Planarity :  0.005   0.033    440
  Dihedral  :  6.233  23.967    336
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 25.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers : 11.11 %
    Allowed  : 22.92 %
    Favored  : 65.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.49), residues: 302
  helix:  1.19 (0.63), residues: 72
  sheet: -1.89 (0.55), residues: 82
  loop : -2.93 (0.50), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 192 
 HIS   0.014   0.003   HIS B 110 
 PHE   0.019   0.002   PHE B 106 
 TYR   0.012   0.002   TYR B 126 
 ARG   0.004   0.001   ARG A 206 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03829 (   94)
  hydrogen bonds       : angle       6.35471 (  300)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       1.35992 (    4)
  covalent geometry    : bond        0.00522 ( 2580)
  covalent geometry    : angle       0.91165 ( 3494)

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

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

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

  604 Ramachandran restraints generated.
    302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 112
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9101 (pp30) cc_final: 0.8318 (pm20)
REVERT: A  115 LYS cc_start: 0.7864 (tptm) cc_final: 0.7303 (mttm)
REVERT: A  121 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5904 (tpt)
REVERT: A  139 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7921 (tp-100)
REVERT: A  211 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8189 (mtp85)
REVERT: A  213 HIS cc_start: 0.7484 (m90) cc_final: 0.7219 (m-70)
REVERT: A  221 GLU cc_start: 0.8070 (pp20) cc_final: 0.7857 (pp20)
REVERT: A  230 TYR cc_start: 0.9163 (m-80) cc_final: 0.8479 (m-80)
REVERT: A  232 VAL cc_start: 0.9093 (t) cc_final: 0.8628 (m)
REVERT: A  236 ILE cc_start: 0.9299 (mt) cc_final: 0.8838 (tp)
REVERT: A  239 ASP cc_start: 0.8796 (m-30) cc_final: 0.8561 (m-30)
REVERT: B  116 LYS cc_start: 0.7077 (pmtt) cc_final: 0.6510 (ptmm)
REVERT: B  120 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8351 (mp)
REVERT: B  124 GLN cc_start: 0.8268 (mp10) cc_final: 0.7933 (tm-30)
REVERT: B  126 TYR cc_start: 0.6178 (m-10) cc_final: 0.5394 (m-80)
REVERT: B  135 PRO cc_start: 0.9542 (Cg_endo) cc_final: 0.9150 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8663 (mp0) cc_final: 0.8452 (mp0)
REVERT: B  195 GLU cc_start: 0.7583 (tt0) cc_final: 0.7272 (tt0)
REVERT: B  211 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.8013 (mtp85)
REVERT: B  236 ILE cc_start: 0.9222 (mt) cc_final: 0.8914 (tp)
REVERT: B  239 ASP cc_start: 0.8868 (m-30) cc_final: 0.8507 (m-30)
  outliers start: 32
  outliers final: 24
  residues processed: 123
  average time/residue: 0.1918
  time to fit residues: 26.6552
Evaluate side-chains
  134 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 HIS
Chi-restraints excluded: chain A residue   94 PHE
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  106 PHE
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  121 MET
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  134 MET
Chi-restraints excluded: chain A residue  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 A residue  234 LEU
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  118 GLN
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  169 MET
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 7 optimal weight:   20.0000
   chunk 6 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0070
   chunk 19 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.7000

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 110 HIS ** 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 = 0.3739 r_free = 0.3739 target = 0.115060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.092269 restraints weight = 7105.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.095047 restraints weight = 4084.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.096823 restraints weight = 2879.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.7280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   2582  Z= 0.165
  Angle     :  0.965  10.853   3498  Z= 0.473
  Chirality :  0.057   0.228    388
  Planarity :  0.005   0.035    440
  Dihedral  :  6.108  23.778    336
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.59 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 30.56 %
    Favored  : 63.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.49), residues: 302
  helix:  1.09 (0.64), residues: 72
  sheet: -1.96 (0.53), residues: 86
  loop : -2.94 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 182 
 HIS   0.012   0.002   HIS B 110 
 PHE   0.017   0.002   PHE B 106 
 TYR   0.012   0.001   TYR B 171 
 ARG   0.010   0.001   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03659 (   94)
  hydrogen bonds       : angle       6.63575 (  300)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       1.45058 (    4)
  covalent geometry    : bond        0.00380 ( 2580)
  covalent geometry    : angle       0.96393 ( 3494)

*********************** 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
  145 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9067 (pp30) cc_final: 0.8535 (pp30)
REVERT: A  115 LYS cc_start: 0.7816 (tptm) cc_final: 0.7472 (mttm)
REVERT: A  121 MET cc_start: 0.6395 (tpp) cc_final: 0.6141 (tpt)
REVERT: A  152 MET cc_start: 0.6645 (mmm) cc_final: 0.6408 (mmm)
REVERT: A  211 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8252 (mtp85)
REVERT: A  213 HIS cc_start: 0.7316 (m90) cc_final: 0.6954 (m90)
REVERT: A  223 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8543 (mm-40)
REVERT: A  230 TYR cc_start: 0.9119 (m-80) cc_final: 0.8184 (m-80)
REVERT: A  232 VAL cc_start: 0.9231 (t) cc_final: 0.8842 (m)
REVERT: A  236 ILE cc_start: 0.9269 (mt) cc_final: 0.8750 (tp)
REVERT: B  116 LYS cc_start: 0.6945 (pmtt) cc_final: 0.6402 (ptmm)
REVERT: B  120 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8404 (mp)
REVERT: B  124 GLN cc_start: 0.8373 (mp10) cc_final: 0.8042 (tm-30)
REVERT: B  126 TYR cc_start: 0.6352 (m-10) cc_final: 0.5728 (m-80)
REVERT: B  135 PRO cc_start: 0.9343 (Cg_endo) cc_final: 0.8830 (Cg_exo)
REVERT: B  136 GLU cc_start: 0.8646 (mp0) cc_final: 0.8363 (mp0)
REVERT: B  147 MET cc_start: 0.8222 (tpp) cc_final: 0.7986 (tpp)
REVERT: B  195 GLU cc_start: 0.7493 (tt0) cc_final: 0.7122 (tt0)
REVERT: B  202 GLU cc_start: 0.8050 (tp30) cc_final: 0.7781 (tp30)
REVERT: B  211 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.8038 (mmp80)
REVERT: B  212 GLN cc_start: 0.8716 (mp10) cc_final: 0.8305 (mp10)
REVERT: B  236 ILE cc_start: 0.9208 (mt) cc_final: 0.8816 (tp)
REVERT: B  237 VAL cc_start: 0.8998 (m) cc_final: 0.8292 (p)
REVERT: B  239 ASP cc_start: 0.8994 (m-30) cc_final: 0.8533 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 132
  average time/residue: 0.1955
  time to fit residues: 29.1167
Evaluate side-chains
  132 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  120 LEU
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  190 LEU
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 20 optimal weight:    0.6980
   chunk 7 optimal weight:    9.9990
   chunk 27 optimal weight:   30.0000
   chunk 2 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    4.3388

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 197 GLN
A 235 HIS
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.111574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.089074 restraints weight = 7200.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.091862 restraints weight = 4057.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.093658 restraints weight = 2820.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.7536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078   2582  Z= 0.240
  Angle     :  1.060  14.190   3498  Z= 0.513
  Chirality :  0.060   0.242    388
  Planarity :  0.006   0.046    440
  Dihedral  :  6.518  23.101    336
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 27.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.25 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 31.94 %
    Favored  : 61.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.50), residues: 302
  helix:  1.22 (0.66), residues: 72
  sheet: -1.67 (0.54), residues: 94
  loop : -2.92 (0.52), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 192 
 HIS   0.013   0.003   HIS A 110 
 PHE   0.041   0.003   PHE B 204 
 TYR   0.009   0.002   TYR B 230 
 ARG   0.009   0.001   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03907 (   94)
  hydrogen bonds       : angle       6.73056 (  300)
  SS BOND              : bond        0.00052 (    2)
  SS BOND              : angle       1.33061 (    4)
  covalent geometry    : bond        0.00574 ( 2580)
  covalent geometry    : angle       1.06011 ( 3494)

********************** 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
  129 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9166 (pp30) cc_final: 0.8637 (pp30)
REVERT: A  115 LYS cc_start: 0.7878 (tptm) cc_final: 0.7465 (mttm)
REVERT: A  121 MET cc_start: 0.6148 (tpp) cc_final: 0.5923 (tpt)
REVERT: A  193 LYS cc_start: 0.7289 (mmtm) cc_final: 0.6938 (mmtp)
REVERT: A  211 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.8222 (mtp85)
REVERT: A  221 GLU cc_start: 0.8092 (pp20) cc_final: 0.7885 (pp20)
REVERT: A  232 VAL cc_start: 0.8946 (t) cc_final: 0.8696 (m)
REVERT: A  236 ILE cc_start: 0.9260 (mt) cc_final: 0.8807 (tp)
REVERT: B  116 LYS cc_start: 0.7051 (pmtt) cc_final: 0.6461 (ptmm)
REVERT: B  120 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8448 (mp)
REVERT: B  124 GLN cc_start: 0.8322 (mp10) cc_final: 0.8038 (tm-30)
REVERT: B  126 TYR cc_start: 0.5737 (m-10) cc_final: 0.5244 (m-80)
REVERT: B  135 PRO cc_start: 0.9492 (Cg_endo) cc_final: 0.8969 (Cg_exo)
REVERT: B  170 ARG cc_start: 0.9028 (mmt90) cc_final: 0.8559 (mmt-90)
REVERT: B  195 GLU cc_start: 0.7629 (tt0) cc_final: 0.7353 (tt0)
REVERT: B  207 TYR cc_start: 0.5183 (p90) cc_final: 0.4970 (p90)
REVERT: B  211 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8098 (mmp80)
REVERT: B  236 ILE cc_start: 0.9232 (mt) cc_final: 0.8907 (tp)
REVERT: B  239 ASP cc_start: 0.8968 (m-30) cc_final: 0.8600 (m-30)
  outliers start: 20
  outliers final: 18
  residues processed: 116
  average time/residue: 0.2061
  time to fit residues: 26.8730
Evaluate side-chains
  129 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
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  120 LEU
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  227 ILE
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  106 PHE
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  149 CYS
Chi-restraints excluded: chain B residue  155 TYR
Chi-restraints excluded: chain B residue  234 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 5 optimal weight:    0.2980
   chunk 16 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    2.2386

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** 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 = 0.3740 r_free = 0.3740 target = 0.114665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.091404 restraints weight = 7081.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.094132 restraints weight = 4033.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.095991 restraints weight = 2840.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.7673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   2582  Z= 0.186
  Angle     :  1.004  12.764   3498  Z= 0.492
  Chirality :  0.058   0.226    388
  Planarity :  0.006   0.053    440
  Dihedral  :  6.371  23.227    336
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 21.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.92 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 31.60 %
    Favored  : 61.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.50), residues: 302
  helix:  1.08 (0.66), residues: 72
  sheet: -1.68 (0.55), residues: 94
  loop : -2.98 (0.51), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 182 
 HIS   0.012   0.002   HIS B 110 
 PHE   0.033   0.002   PHE B 204 
 TYR   0.010   0.002   TYR B 171 
 ARG   0.010   0.001   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03863 (   94)
  hydrogen bonds       : angle       6.91598 (  300)
  SS BOND              : bond        0.00089 (    2)
  SS BOND              : angle       1.23867 (    4)
  covalent geometry    : bond        0.00453 ( 2580)
  covalent geometry    : angle       1.00328 ( 3494)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1370.92 seconds
wall clock time: 24 minutes 25.51 seconds (1465.51 seconds total)