Starting phenix.real_space_refine
on Sun May 11 09:35:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8izf_35863/05_2025/8izf_35863.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8izf_35863/05_2025/8izf_35863.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8izf_35863/05_2025/8izf_35863.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8izf_35863/05_2025/8izf_35863.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8izf_35863/05_2025/8izf_35863.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8izf_35863/05_2025/8izf_35863.cif"
  }
  resolution = 3.85
  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=   0.004 sd=   0.052
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      38      5.16       5
     C    5088      2.51       5
     N    1202      2.21       5
     O    1264      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7594
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2670
          Classifications: {'peptide': 315}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 306}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1087
          Classifications: {'peptide': 132}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'6PL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 12
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 5.55, per 1000 atoms: 0.73
  Number of scatterers: 7594
  At special positions: 0
  Unit cell: (110.416, 101.84, 100.768, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       2     15.00
     O    1264      8.00
     N    1202      7.00
     C    5088      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 102 " - pdb=" SG  CYS B 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 102 " - pdb=" SG  CYS D 142 " distance=2.03

  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: 1.71
  Conformation dependent library (CDL) restraints added in 937.4 milliseconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 2 sheets defined
      67.0% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 82
      removed outlier: 3.530A  pdb=" N   PHE A  75 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 100
    Processing helix  chain 'A' and resid 109 through 115
    Processing helix  chain 'A' and resid 130 through 162
      Proline residue:  A 157  - end of helix
    Processing helix  chain 'A' and resid 167 through 196
      Proline residue:  A 188  - end of helix
    Processing helix  chain 'A' and resid 205 through 209
    Processing helix  chain 'A' and resid 217 through 241
    Processing helix  chain 'A' and resid 249 through 269
    Processing helix  chain 'A' and resid 275 through 298
      removed outlier: 3.786A  pdb=" N   LEU A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 335
      removed outlier: 3.947A  pdb=" N   TYR A 320 " --> pdb=" O   TYR A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 384
      removed outlier: 3.881A  pdb=" N   ILE A 356 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 47
    Processing helix  chain 'B' and resid 48 through 52
      removed outlier: 3.736A  pdb=" N   HIS B  52 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 48 through 52'
    Processing helix  chain 'B' and resid 76 through 92
      removed outlier: 3.541A  pdb=" N   TYR B  92 " --> pdb=" O   ILE B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 142
      removed outlier: 3.523A  pdb=" N   VAL B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 82
    Processing helix  chain 'C' and resid 84 through 100
    Processing helix  chain 'C' and resid 109 through 115
    Processing helix  chain 'C' and resid 130 through 162
      Proline residue:  C 157  - end of helix
    Processing helix  chain 'C' and resid 167 through 196
      Proline residue:  C 188  - end of helix
    Processing helix  chain 'C' and resid 205 through 209
    Processing helix  chain 'C' and resid 217 through 241
    Processing helix  chain 'C' and resid 249 through 269
    Processing helix  chain 'C' and resid 275 through 298
      removed outlier: 3.786A  pdb=" N   LEU C 288 " --> pdb=" O   VAL C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 335
      removed outlier: 3.946A  pdb=" N   TYR C 320 " --> pdb=" O   TYR C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 384
      removed outlier: 3.881A  pdb=" N   ILE C 356 " --> pdb=" O   ILE C 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 47
    Processing helix  chain 'D' and resid 48 through 52
      removed outlier: 3.736A  pdb=" N   HIS D  52 " --> pdb=" O   TYR D  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 48 through 52'
    Processing helix  chain 'D' and resid 76 through 92
      removed outlier: 3.541A  pdb=" N   TYR D  92 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 142
      removed outlier: 3.524A  pdb=" N   VAL D 138 " --> pdb=" O   ASP D 134 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 59
      removed outlier: 3.616A  pdb=" N   VAL B 129 " --> pdb=" O   ILE B  65 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 59
      removed outlier: 3.616A  pdb=" N   VAL D 129 " --> pdb=" O   ILE D  65 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1434 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.91

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1096
        1.32 -     1.44: 2532
        1.44 -     1.57: 4158
        1.57 -     1.70: 2
        1.70 -     1.83: 58
  Bond restraints: 7846
  Sorted by residual:
  bond pdb=" C31 6PL D 201 "
       pdb=" O2  6PL D 201 "
    ideal  model  delta    sigma   weight residual
    1.330  1.430 -0.100 2.00e-02 2.50e+03 2.52e+01
  bond pdb=" C31 6PL B 201 "
       pdb=" O2  6PL B 201 "
    ideal  model  delta    sigma   weight residual
    1.330  1.430 -0.100 2.00e-02 2.50e+03 2.51e+01
  bond pdb=" C11 6PL D 201 "
       pdb=" O3  6PL D 201 "
    ideal  model  delta    sigma   weight residual
    1.327  1.426 -0.099 2.00e-02 2.50e+03 2.47e+01
  bond pdb=" C11 6PL B 201 "
       pdb=" O3  6PL B 201 "
    ideal  model  delta    sigma   weight residual
    1.327  1.426 -0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" CA  PHE A 343 "
       pdb=" CB  PHE A 343 "
    ideal  model  delta    sigma   weight residual
    1.530  1.462  0.068 1.69e-02 3.50e+03 1.62e+01
  ... (remaining 7841 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.86: 10531
        3.86 -     7.73: 101
        7.73 -    11.59: 8
       11.59 -    15.46: 8
       15.46 -    19.32: 4
  Bond angle restraints: 10652
  Sorted by residual:
  angle pdb=" N   PHE C 343 "
        pdb=" CA  PHE C 343 "
        pdb=" C   PHE C 343 "
      ideal   model   delta    sigma   weight residual
     110.80  130.12  -19.32 2.13e+00 2.20e-01 8.23e+01
  angle pdb=" N   PHE A 343 "
        pdb=" CA  PHE A 343 "
        pdb=" C   PHE A 343 "
      ideal   model   delta    sigma   weight residual
     110.80  130.08  -19.28 2.13e+00 2.20e-01 8.20e+01
  angle pdb=" N   LYS C 247 "
        pdb=" CA  LYS C 247 "
        pdb=" C   LYS C 247 "
      ideal   model   delta    sigma   weight residual
     110.24   98.33   11.91 1.41e+00 5.03e-01 7.13e+01
  angle pdb=" N   LYS A 247 "
        pdb=" CA  LYS A 247 "
        pdb=" C   LYS A 247 "
      ideal   model   delta    sigma   weight residual
     110.24   98.35   11.89 1.41e+00 5.03e-01 7.11e+01
  angle pdb=" N   MET A 140 "
        pdb=" CA  MET A 140 "
        pdb=" C   MET A 140 "
      ideal   model   delta    sigma   weight residual
     111.36  103.42    7.94 1.09e+00 8.42e-01 5.31e+01
  ... (remaining 10647 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.05: 3954
       18.05 -    36.09: 412
       36.09 -    54.14: 100
       54.14 -    72.19: 16
       72.19 -    90.24: 16
  Dihedral angle restraints: 4498
    sinusoidal: 1834
      harmonic: 2664
  Sorted by residual:
  dihedral pdb=" CA  GLU D 118 "
           pdb=" C   GLU D 118 "
           pdb=" N   ASP D 119 "
           pdb=" CA  ASP D 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  GLU B 118 "
           pdb=" C   GLU B 118 "
           pdb=" N   ASP B 119 "
           pdb=" CA  ASP B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.70   21.30     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  CYS B  53 "
           pdb=" CB  CYS B  53 "
           pdb=" SG  CYS B  53 "
           pdb=" SG  CYS B  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    2.17  -75.17     1      2.00e+01 2.50e-03 1.79e+01
  ... (remaining 4495 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1107
       0.118 -    0.236: 27
       0.236 -    0.354: 2
       0.354 -    0.472: 0
       0.472 -    0.590: 2
  Chirality restraints: 1138
  Sorted by residual:
  chirality pdb=" CA  PHE C 343 "
            pdb=" N   PHE C 343 "
            pdb=" C   PHE C 343 "
            pdb=" CB  PHE C 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.59 2.00e-01 2.50e+01 8.71e+00
  chirality pdb=" CA  PHE A 343 "
            pdb=" N   PHE A 343 "
            pdb=" C   PHE A 343 "
            pdb=" CB  PHE A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.92    0.59 2.00e-01 2.50e+01 8.67e+00
  chirality pdb=" CA  LYS C 247 "
            pdb=" N   LYS C 247 "
            pdb=" C   LYS C 247 "
            pdb=" CB  LYS C 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.89e+00
  ... (remaining 1135 not shown)

  Planarity restraints: 1296
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 139 "   -0.019 2.00e-02 2.50e+03   3.87e-02 1.49e+01
        pdb=" C   TYR A 139 "    0.067 2.00e-02 2.50e+03
        pdb=" O   TYR A 139 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   MET A 140 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 139 "    0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   TYR C 139 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   TYR C 139 "    0.026 2.00e-02 2.50e+03
        pdb=" N   MET C 140 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D  77 "   -0.016 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   LYS D  77 "    0.057 2.00e-02 2.50e+03
        pdb=" O   LYS D  77 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ARG D  78 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1293 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.54: 65
        2.54 -     3.13: 6462
        3.13 -     3.72: 12006
        3.72 -     4.31: 15506
        4.31 -     4.90: 25341
  Nonbonded interactions: 59380
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 103 "
            pdb=" OH  TYR D 148 "
     model   vdw
     1.945 3.040
  nonbonded pdb=" OH  TYR B 148 "
            pdb=" O   ILE D 103 "
     model   vdw
     1.952 3.040
  nonbonded pdb=" O   LYS A 244 "
            pdb=" O   PRO A 245 "
     model   vdw
     2.010 3.040
  nonbonded pdb=" O   LYS C 244 "
            pdb=" O   PRO C 245 "
     model   vdw
     2.011 3.040
  nonbonded pdb=" OG  SER A 186 "
            pdb=" OD2 ASP A 283 "
     model   vdw
     2.168 3.040
  ... (remaining 59375 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             0.800
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.940
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
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      :  0.006   0.100   7850  Z= 0.334
  Angle     :  1.097  19.322  10660  Z= 0.624
  Chirality :  0.057   0.590   1138
  Planarity :  0.006   0.063   1296
  Dihedral  : 16.149  90.235   2778
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 21.89
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  9.48 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  :  1.74 %
    Favored  : 95.53 %
  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: -1.59 (0.27), residues: 886
  helix:  0.25 (0.20), residues: 562
  sheet: -1.68 (0.58), residues: 58
  loop : -3.81 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D  50 
 HIS   0.008   0.001   HIS A 249 
 PHE   0.020   0.002   PHE A 271 
 TYR   0.032   0.002   TYR C 279 
 ARG   0.011   0.001   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13092 (  486)
  hydrogen bonds       : angle       6.44811 ( 1434)
  SS BOND              : bond        0.00184 (    4)
  SS BOND              : angle       2.55366 (    8)
  covalent geometry    : bond        0.00617 ( 7846)
  covalent geometry    : angle       1.09513 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 294
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8276 (p-90) cc_final: 0.7844 (p-90)
REVERT: A  168 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6197 (m90)
REVERT: A  174 MET cc_start: 0.8632 (mmt) cc_final: 0.8164 (mmt)
REVERT: A  182 TYR cc_start: 0.7918 (p90) cc_final: 0.7554 (t80)
REVERT: A  236 CYS cc_start: 0.8676 (p) cc_final: 0.8464 (p)
REVERT: A  251 GLU cc_start: 0.7857 (pm20) cc_final: 0.7460 (pm20)
REVERT: A  289 LEU cc_start: 0.8881 (tp) cc_final: 0.8583 (tt)
REVERT: A  334 ARG cc_start: 0.7006 (tmt170) cc_final: 0.6782 (tpt170)
REVERT: A  343 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7782 (t80)
REVERT: A  346 GLN cc_start: 0.8589 (mp10) cc_final: 0.8219 (mp10)
REVERT: C   84 TRP cc_start: 0.8268 (p-90) cc_final: 0.7829 (p-90)
REVERT: C  168 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6175 (m90)
REVERT: C  174 MET cc_start: 0.8753 (mmt) cc_final: 0.8269 (mmt)
REVERT: C  236 CYS cc_start: 0.8675 (p) cc_final: 0.8460 (p)
REVERT: C  251 GLU cc_start: 0.7866 (pm20) cc_final: 0.7509 (pm20)
REVERT: C  334 ARG cc_start: 0.6939 (tmt170) cc_final: 0.6230 (ttt180)
REVERT: C  343 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7799 (t80)
REVERT: C  346 GLN cc_start: 0.8577 (mp10) cc_final: 0.8175 (mp10)
REVERT: D   65 ILE cc_start: 0.9318 (pt) cc_final: 0.9083 (pt)
  outliers start: 22
  outliers final: 4
  residues processed: 306
  average time/residue: 0.1658
  time to fit residues: 69.7116
Evaluate side-chains
  212 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 204
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  343 PHE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  364 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 66 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0170
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
A 332 GLN
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 HIS
C 332 GLN
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.132077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.109771 restraints weight = 16692.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.112879 restraints weight = 9674.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.114902 restraints weight = 6754.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7850  Z= 0.151
  Angle     :  0.724  13.409  10660  Z= 0.373
  Chirality :  0.043   0.140   1138
  Planarity :  0.005   0.056   1296
  Dihedral  :  9.685  54.833   1084
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 16.00 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.28), residues: 886
  helix:  0.93 (0.21), residues: 544
  sheet: -1.69 (0.57), residues: 58
  loop : -3.48 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  68 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.032   0.002   PHE A 158 
 TYR   0.030   0.002   TYR C 182 
 ARG   0.003   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04869 (  486)
  hydrogen bonds       : angle       5.26314 ( 1434)
  SS BOND              : bond        0.00190 (    4)
  SS BOND              : angle       1.80124 (    8)
  covalent geometry    : bond        0.00327 ( 7846)
  covalent geometry    : angle       0.72291 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 249
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8444 (p-90) cc_final: 0.8057 (p-90)
REVERT: A  140 MET cc_start: 0.8492 (tpp) cc_final: 0.7812 (tpp)
REVERT: A  168 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.6608 (m90)
REVERT: A  203 ASN cc_start: 0.8562 (t0) cc_final: 0.8333 (t0)
REVERT: A  233 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8408 (tt0)
REVERT: A  332 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7789 (mt0)
REVERT: A  334 ARG cc_start: 0.6465 (tmt170) cc_final: 0.5638 (ttt180)
REVERT: A  343 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7894 (t80)
REVERT: A  357 VAL cc_start: 0.7658 (t) cc_final: 0.7453 (p)
REVERT: A  370 TYR cc_start: 0.8083 (t80) cc_final: 0.7841 (t80)
REVERT: B   80 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7010 (tt0)
REVERT: B  148 TYR cc_start: 0.7967 (m-80) cc_final: 0.7647 (m-80)
REVERT: C   84 TRP cc_start: 0.8429 (p-90) cc_final: 0.8043 (p-90)
REVERT: C  168 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.6575 (m90)
REVERT: C  203 ASN cc_start: 0.8724 (t0) cc_final: 0.8490 (t0)
REVERT: C  332 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7741 (mt0)
REVERT: C  334 ARG cc_start: 0.6498 (tmt170) cc_final: 0.5676 (ttt180)
REVERT: C  343 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7902 (t80)
REVERT: C  370 TYR cc_start: 0.8074 (t80) cc_final: 0.7760 (t80)
REVERT: D   65 ILE cc_start: 0.9314 (pt) cc_final: 0.9089 (pt)
REVERT: D   80 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7089 (mt-10)
  outliers start: 35
  outliers final: 23
  residues processed: 266
  average time/residue: 0.1514
  time to fit residues: 56.8303
Evaluate side-chains
  234 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 205
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  175 GLU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  175 GLU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  237 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  332 GLN
Chi-restraints excluded: chain C residue  339 TYR
Chi-restraints excluded: chain C residue  343 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue  126 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
A 332 GLN
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 113 HIS
C  82 HIS
C 332 GLN
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 113 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.124727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.103037 restraints weight = 17477.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.105083 restraints weight = 10213.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.106014 restraints weight = 7983.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   7850  Z= 0.303
  Angle     :  0.822  12.795  10660  Z= 0.425
  Chirality :  0.048   0.230   1138
  Planarity :  0.006   0.057   1296
  Dihedral  :  9.528  59.234   1082
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.61 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 18.73 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.28), residues: 886
  helix:  0.77 (0.21), residues: 552
  sheet: -1.34 (0.58), residues: 56
  loop : -3.68 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP C  72 
 HIS   0.009   0.002   HIS C 256 
 PHE   0.026   0.002   PHE A 158 
 TYR   0.034   0.002   TYR C 279 
 ARG   0.004   0.001   ARG D  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05269 (  486)
  hydrogen bonds       : angle       5.28583 ( 1434)
  SS BOND              : bond        0.00327 (    4)
  SS BOND              : angle       2.01987 (    8)
  covalent geometry    : bond        0.00693 ( 7846)
  covalent geometry    : angle       0.82018 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 212
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8435 (p-90) cc_final: 0.8111 (p-90)
REVERT: A  140 MET cc_start: 0.8643 (tpp) cc_final: 0.8372 (tpp)
REVERT: A  168 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.6727 (m90)
REVERT: A  203 ASN cc_start: 0.8787 (t0) cc_final: 0.8559 (t0)
REVERT: A  224 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.6961 (t80)
REVERT: A  233 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8023 (tm-30)
REVERT: A  248 ASP cc_start: 0.7722 (t70) cc_final: 0.6874 (t0)
REVERT: A  289 LEU cc_start: 0.8960 (tp) cc_final: 0.8690 (tt)
REVERT: A  332 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7874 (mt0)
REVERT: A  334 ARG cc_start: 0.6792 (tmt170) cc_final: 0.5896 (ttt180)
REVERT: A  343 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7834 (t80)
REVERT: B   38 GLU cc_start: 0.8338 (tp30) cc_final: 0.8012 (tp30)
REVERT: B   67 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9002 (tt)
REVERT: B  149 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7422 (p90)
REVERT: C   84 TRP cc_start: 0.8425 (p-90) cc_final: 0.8085 (p-90)
REVERT: C  168 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.6735 (m90)
REVERT: C  203 ASN cc_start: 0.8766 (t0) cc_final: 0.8539 (t0)
REVERT: C  224 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.6949 (t80)
REVERT: C  332 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7937 (mt0)
REVERT: C  334 ARG cc_start: 0.6723 (tmt170) cc_final: 0.5809 (ttt180)
REVERT: C  343 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7888 (t80)
REVERT: D   38 GLU cc_start: 0.8157 (tp30) cc_final: 0.7824 (tp30)
REVERT: D   67 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8991 (tt)
REVERT: D  149 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7371 (p90)
  outliers start: 59
  outliers final: 41
  residues processed: 250
  average time/residue: 0.1530
  time to fit residues: 54.6420
Evaluate side-chains
  266 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 213
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  175 GLU
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  175 GLU
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  237 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  325 ILE
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  332 GLN
Chi-restraints excluded: chain C residue  343 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain C residue  378 VAL
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 47 optimal weight:    0.3980
   chunk 41 optimal weight:    7.9990
   chunk 19 optimal weight:    0.5980
   chunk 4 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  82 HIS
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 GLN
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  82 HIS
** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 GLN
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.119573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.097968 restraints weight = 17792.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.099710 restraints weight = 10920.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.100649 restraints weight = 8526.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7850  Z= 0.156
  Angle     :  0.707  11.589  10660  Z= 0.361
  Chirality :  0.043   0.188   1138
  Planarity :  0.005   0.053   1296
  Dihedral  :  8.769  59.958   1082
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 23.45 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.28), residues: 886
  helix:  0.90 (0.21), residues: 552
  sheet: -0.67 (0.58), residues: 52
  loop : -3.77 (0.32), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C  72 
 HIS   0.008   0.001   HIS C  82 
 PHE   0.029   0.002   PHE C 158 
 TYR   0.025   0.002   TYR C 182 
 ARG   0.003   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04757 (  486)
  hydrogen bonds       : angle       4.98741 ( 1434)
  SS BOND              : bond        0.00223 (    4)
  SS BOND              : angle       1.50358 (    8)
  covalent geometry    : bond        0.00349 ( 7846)
  covalent geometry    : angle       0.70595 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 236
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.8537 (tpp) cc_final: 0.8222 (tpp)
REVERT: A  168 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.6761 (m90)
REVERT: A  203 ASN cc_start: 0.8730 (t0) cc_final: 0.8413 (t0)
REVERT: A  224 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.6795 (t80)
REVERT: A  233 GLN cc_start: 0.8887 (tm-30) cc_final: 0.7941 (tm-30)
REVERT: A  248 ASP cc_start: 0.7485 (t70) cc_final: 0.6955 (t0)
REVERT: A  251 GLU cc_start: 0.7572 (pm20) cc_final: 0.7324 (pm20)
REVERT: A  334 ARG cc_start: 0.6944 (tmt170) cc_final: 0.5929 (ttt180)
REVERT: A  343 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7869 (t80)
REVERT: B   38 GLU cc_start: 0.8213 (tp30) cc_final: 0.7864 (tp30)
REVERT: C  168 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.6771 (m90)
REVERT: C  203 ASN cc_start: 0.8751 (t0) cc_final: 0.8456 (t0)
REVERT: C  224 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.6825 (t80)
REVERT: C  248 ASP cc_start: 0.7583 (t0) cc_final: 0.7052 (t0)
REVERT: C  251 GLU cc_start: 0.7593 (pm20) cc_final: 0.7385 (pm20)
REVERT: C  334 ARG cc_start: 0.6860 (tmt170) cc_final: 0.5877 (ttt180)
REVERT: C  343 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7917 (t80)
REVERT: D   38 GLU cc_start: 0.8222 (tp30) cc_final: 0.7882 (tp30)
REVERT: D   92 TYR cc_start: 0.8731 (m-10) cc_final: 0.8350 (m-10)
  outliers start: 54
  outliers final: 36
  residues processed: 268
  average time/residue: 0.1450
  time to fit residues: 55.2783
Evaluate side-chains
  256 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 214
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  168 HIS
Chi-restraints excluded: chain A residue  175 GLU
Chi-restraints excluded: chain A residue  193 CYS
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  175 GLU
Chi-restraints excluded: chain C residue  193 CYS
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  343 PHE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   37 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 75 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 332 GLN
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 332 GLN
** D  52 HIS ** 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 = 0.3724 r_free = 0.3724 target = 0.122032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.100155 restraints weight = 17352.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.101807 restraints weight = 10637.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.102745 restraints weight = 8450.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7850  Z= 0.143
  Angle     :  0.682  10.850  10660  Z= 0.347
  Chirality :  0.043   0.179   1138
  Planarity :  0.005   0.052   1296
  Dihedral  :  8.308  58.549   1082
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 24.81 %
    Favored  : 67.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.28), residues: 886
  helix:  1.00 (0.21), residues: 552
  sheet: -0.87 (0.59), residues: 56
  loop : -3.73 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  84 
 HIS   0.003   0.001   HIS B 113 
 PHE   0.029   0.001   PHE C 158 
 TYR   0.020   0.002   TYR C 182 
 ARG   0.005   0.000   ARG D  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04319 (  486)
  hydrogen bonds       : angle       4.74110 ( 1434)
  SS BOND              : bond        0.00634 (    4)
  SS BOND              : angle       2.49091 (    8)
  covalent geometry    : bond        0.00318 ( 7846)
  covalent geometry    : angle       0.67870 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 232
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  203 ASN cc_start: 0.8621 (t0) cc_final: 0.8327 (t0)
REVERT: A  224 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7047 (t80)
REVERT: A  233 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8198 (tm-30)
REVERT: A  248 ASP cc_start: 0.7473 (t70) cc_final: 0.6781 (t0)
REVERT: A  251 GLU cc_start: 0.7440 (pm20) cc_final: 0.7055 (pm20)
REVERT: A  332 GLN cc_start: 0.8439 (mt0) cc_final: 0.8181 (mt0)
REVERT: A  334 ARG cc_start: 0.6834 (tmt170) cc_final: 0.5781 (ttt180)
REVERT: A  343 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.7656 (t80)
REVERT: B   38 GLU cc_start: 0.8223 (tp30) cc_final: 0.7910 (tp30)
REVERT: B   44 THR cc_start: 0.9332 (t) cc_final: 0.8575 (t)
REVERT: B  147 ILE cc_start: 0.9511 (tp) cc_final: 0.9310 (tp)
REVERT: B  149 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7425 (p90)
REVERT: C  203 ASN cc_start: 0.8603 (t0) cc_final: 0.8257 (t0)
REVERT: C  224 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7106 (t80)
REVERT: C  248 ASP cc_start: 0.7439 (t0) cc_final: 0.6638 (t0)
REVERT: C  251 GLU cc_start: 0.7471 (pm20) cc_final: 0.7116 (pm20)
REVERT: C  332 GLN cc_start: 0.8474 (mt0) cc_final: 0.8244 (mt0)
REVERT: C  334 ARG cc_start: 0.6857 (tmt170) cc_final: 0.5788 (ttt180)
REVERT: D   38 GLU cc_start: 0.8246 (tp30) cc_final: 0.7935 (tp30)
REVERT: D  149 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7384 (p90)
  outliers start: 59
  outliers final: 36
  residues processed: 268
  average time/residue: 0.1485
  time to fit residues: 57.0292
Evaluate side-chains
  262 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 221
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  193 CYS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  193 CYS
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  325 ILE
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 47 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 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 = 0.3725 r_free = 0.3725 target = 0.122120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.100295 restraints weight = 17462.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.102168 restraints weight = 10689.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.103108 restraints weight = 8334.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7850  Z= 0.143
  Angle     :  0.705  10.707  10660  Z= 0.358
  Chirality :  0.043   0.159   1138
  Planarity :  0.005   0.051   1296
  Dihedral  :  7.698  57.881   1076
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 26.67 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.28), residues: 886
  helix:  0.96 (0.21), residues: 560
  sheet: -0.76 (0.59), residues: 56
  loop : -3.57 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  84 
 HIS   0.003   0.001   HIS D 113 
 PHE   0.035   0.002   PHE C 158 
 TYR   0.021   0.002   TYR D  92 
 ARG   0.004   0.000   ARG D  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04323 (  486)
  hydrogen bonds       : angle       4.76602 ( 1434)
  SS BOND              : bond        0.00219 (    4)
  SS BOND              : angle       2.40125 (    8)
  covalent geometry    : bond        0.00321 ( 7846)
  covalent geometry    : angle       0.70232 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 236
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8381 (p-90) cc_final: 0.8148 (p-90)
REVERT: A  203 ASN cc_start: 0.8567 (t0) cc_final: 0.8272 (t0)
REVERT: A  224 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7040 (t80)
REVERT: A  233 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8637 (tm-30)
REVERT: A  248 ASP cc_start: 0.7433 (t70) cc_final: 0.6693 (t0)
REVERT: A  251 GLU cc_start: 0.7245 (pm20) cc_final: 0.6863 (pm20)
REVERT: A  332 GLN cc_start: 0.8358 (mt0) cc_final: 0.7606 (mt0)
REVERT: A  334 ARG cc_start: 0.6876 (tmt170) cc_final: 0.5778 (ttt180)
REVERT: B  149 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7355 (p90)
REVERT: C  140 MET cc_start: 0.8718 (tpp) cc_final: 0.8238 (tpp)
REVERT: C  203 ASN cc_start: 0.8605 (t0) cc_final: 0.8285 (t0)
REVERT: C  224 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7048 (t80)
REVERT: C  248 ASP cc_start: 0.7482 (t0) cc_final: 0.6678 (t0)
REVERT: C  251 GLU cc_start: 0.7252 (pm20) cc_final: 0.6884 (pm20)
REVERT: C  332 GLN cc_start: 0.8442 (mt0) cc_final: 0.7610 (mt0)
REVERT: C  334 ARG cc_start: 0.6821 (tmt170) cc_final: 0.5761 (ttt180)
REVERT: D  149 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.7302 (p90)
  outliers start: 51
  outliers final: 39
  residues processed: 266
  average time/residue: 0.1612
  time to fit residues: 60.4820
Evaluate side-chains
  263 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 220
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  193 CYS
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  193 CYS
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  318 ARG
Chi-restraints excluded: chain C residue  330 LEU
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.131247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.107998 restraints weight = 16896.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.111061 restraints weight = 9760.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.113217 restraints weight = 6855.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.4365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7850  Z= 0.147
  Angle     :  0.709  10.498  10660  Z= 0.362
  Chirality :  0.044   0.157   1138
  Planarity :  0.005   0.050   1296
  Dihedral  :  7.379  56.338   1074
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.48 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 27.79 %
    Favored  : 66.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.28), residues: 886
  helix:  1.02 (0.21), residues: 560
  sheet: -0.60 (0.58), residues: 56
  loop : -3.53 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  84 
 HIS   0.002   0.001   HIS C 256 
 PHE   0.033   0.002   PHE C 158 
 TYR   0.020   0.001   TYR B  42 
 ARG   0.004   0.000   ARG D  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04317 (  486)
  hydrogen bonds       : angle       4.72560 ( 1434)
  SS BOND              : bond        0.00166 (    4)
  SS BOND              : angle       2.25029 (    8)
  covalent geometry    : bond        0.00334 ( 7846)
  covalent geometry    : angle       0.70619 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 233
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8451 (p-90) cc_final: 0.8205 (p-90)
REVERT: A  140 MET cc_start: 0.8722 (tpp) cc_final: 0.8289 (tpp)
REVERT: A  203 ASN cc_start: 0.8443 (t0) cc_final: 0.8121 (t0)
REVERT: A  233 GLN cc_start: 0.8826 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: A  334 ARG cc_start: 0.6733 (tmt170) cc_final: 0.5700 (ttt180)
REVERT: B   78 ARG cc_start: 0.8804 (ttp-170) cc_final: 0.8396 (ptm160)
REVERT: B  118 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7763 (tm-30)
REVERT: B  149 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7393 (p90)
REVERT: C  224 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7112 (t80)
REVERT: C  233 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: C  323 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8751 (tp)
REVERT: C  332 GLN cc_start: 0.8349 (mt0) cc_final: 0.8109 (mt0)
REVERT: C  334 ARG cc_start: 0.6702 (tmt170) cc_final: 0.5664 (ttt180)
REVERT: D   44 THR cc_start: 0.9400 (t) cc_final: 0.9177 (t)
REVERT: D  149 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7043 (p90)
  outliers start: 45
  outliers final: 37
  residues processed: 259
  average time/residue: 0.1598
  time to fit residues: 57.6931
Evaluate side-chains
  266 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 225
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  193 CYS
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  318 ARG
Chi-restraints excluded: chain C residue  323 LEU
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.130361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.107386 restraints weight = 17293.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.110472 restraints weight = 9874.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.112608 restraints weight = 6910.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7850  Z= 0.146
  Angle     :  0.715  10.249  10660  Z= 0.364
  Chirality :  0.044   0.167   1138
  Planarity :  0.005   0.050   1296
  Dihedral  :  7.270  56.414   1074
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 29.78 %
    Favored  : 64.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.28), residues: 886
  helix:  1.08 (0.21), residues: 562
  sheet: -0.58 (0.60), residues: 56
  loop : -3.41 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C  84 
 HIS   0.003   0.001   HIS A 256 
 PHE   0.021   0.001   PHE B  24 
 TYR   0.027   0.002   TYR C 182 
 ARG   0.004   0.000   ARG D  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 (  486)
  hydrogen bonds       : angle       4.66114 ( 1434)
  SS BOND              : bond        0.00137 (    4)
  SS BOND              : angle       2.13464 (    8)
  covalent geometry    : bond        0.00331 ( 7846)
  covalent geometry    : angle       0.71331 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 243
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A   84 TRP cc_start: 0.8408 (p-90) cc_final: 0.8142 (p-90)
REVERT: A  140 MET cc_start: 0.8703 (tpp) cc_final: 0.8227 (tpp)
REVERT: A  203 ASN cc_start: 0.8423 (t0) cc_final: 0.8179 (t0)
REVERT: A  233 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8000 (tm-30)
REVERT: A  255 HIS cc_start: 0.7354 (OUTLIER) cc_final: 0.6977 (t-90)
REVERT: A  282 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7996 (tpp)
REVERT: A  323 LEU cc_start: 0.8927 (mm) cc_final: 0.8707 (tp)
REVERT: A  334 ARG cc_start: 0.6726 (tmt170) cc_final: 0.5682 (ttt180)
REVERT: B   44 THR cc_start: 0.9362 (t) cc_final: 0.9126 (t)
REVERT: B   92 TYR cc_start: 0.8542 (m-10) cc_final: 0.8054 (m-10)
REVERT: B  139 GLN cc_start: 0.8215 (mt0) cc_final: 0.7977 (mt0)
REVERT: B  149 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7201 (p90)
REVERT: C  140 MET cc_start: 0.8692 (tpp) cc_final: 0.8410 (tpp)
REVERT: C  233 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8107 (tm-30)
REVERT: C  250 ASN cc_start: 0.7488 (p0) cc_final: 0.7163 (t0)
REVERT: C  323 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8729 (tp)
REVERT: C  332 GLN cc_start: 0.8346 (mt0) cc_final: 0.8119 (mt0)
REVERT: C  334 ARG cc_start: 0.6715 (tmt170) cc_final: 0.5674 (ttt180)
REVERT: D  118 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: D  149 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.6940 (p90)
  outliers start: 45
  outliers final: 34
  residues processed: 268
  average time/residue: 0.1610
  time to fit residues: 60.1028
Evaluate side-chains
  269 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 230
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  255 HIS
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  323 LEU
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 79 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0870
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 342 ASN
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.122485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.100838 restraints weight = 18158.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.102589 restraints weight = 10989.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.103542 restraints weight = 8649.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.4773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7850  Z= 0.145
  Angle     :  0.734  10.082  10660  Z= 0.374
  Chirality :  0.044   0.180   1138
  Planarity :  0.005   0.055   1296
  Dihedral  :  7.147  57.173   1072
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 30.40 %
    Favored  : 64.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.28), residues: 886
  helix:  1.10 (0.22), residues: 564
  sheet: -0.64 (0.62), residues: 56
  loop : -3.36 (0.33), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  84 
 HIS   0.005   0.001   HIS A 319 
 PHE   0.034   0.001   PHE B  24 
 TYR   0.019   0.001   TYR B  42 
 ARG   0.008   0.001   ARG A 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04209 (  486)
  hydrogen bonds       : angle       4.61491 ( 1434)
  SS BOND              : bond        0.00159 (    4)
  SS BOND              : angle       2.03221 (    8)
  covalent geometry    : bond        0.00327 ( 7846)
  covalent geometry    : angle       0.73237 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 237
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8394 (p-90) cc_final: 0.8133 (p-90)
REVERT: A  140 MET cc_start: 0.8725 (tpp) cc_final: 0.8253 (tpp)
REVERT: A  177 MET cc_start: 0.7842 (tpp) cc_final: 0.7049 (tpp)
REVERT: A  203 ASN cc_start: 0.8536 (t0) cc_final: 0.8260 (t0)
REVERT: A  233 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8048 (tm-30)
REVERT: A  255 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.6994 (t-90)
REVERT: A  282 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7990 (tpp)
REVERT: A  323 LEU cc_start: 0.8937 (mm) cc_final: 0.8717 (tp)
REVERT: A  334 ARG cc_start: 0.6862 (tmt170) cc_final: 0.5758 (ttt180)
REVERT: B  139 GLN cc_start: 0.8179 (mt0) cc_final: 0.7955 (mt0)
REVERT: B  149 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.6897 (p90)
REVERT: C  140 MET cc_start: 0.8776 (tpp) cc_final: 0.8319 (tpp)
REVERT: C  177 MET cc_start: 0.7795 (tpp) cc_final: 0.7017 (tpp)
REVERT: C  233 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8015 (tm-30)
REVERT: C  248 ASP cc_start: 0.8085 (t0) cc_final: 0.7052 (t0)
REVERT: C  250 ASN cc_start: 0.7710 (p0) cc_final: 0.7186 (t0)
REVERT: C  251 GLU cc_start: 0.7616 (pm20) cc_final: 0.6823 (pm20)
REVERT: C  332 GLN cc_start: 0.8479 (mt0) cc_final: 0.8241 (mt0)
REVERT: C  334 ARG cc_start: 0.6813 (tmt170) cc_final: 0.5718 (ttt180)
REVERT: D  118 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7926 (tm-30)
REVERT: D  149 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.6959 (p90)
  outliers start: 44
  outliers final: 35
  residues processed: 260
  average time/residue: 0.1526
  time to fit residues: 56.2471
Evaluate side-chains
  269 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 230
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  255 HIS
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 57 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 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 = 0.3722 r_free = 0.3722 target = 0.121850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.099615 restraints weight = 17970.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.102503 restraints weight = 10138.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.103656 restraints weight = 6818.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7850  Z= 0.155
  Angle     :  0.755  10.266  10660  Z= 0.385
  Chirality :  0.045   0.202   1138
  Planarity :  0.005   0.052   1296
  Dihedral  :  7.058  57.647   1070
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 31.39 %
    Favored  : 63.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.28), residues: 886
  helix:  1.15 (0.22), residues: 562
  sheet: -0.58 (0.64), residues: 56
  loop : -3.32 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  84 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.016   0.001   PHE C 271 
 TYR   0.031   0.002   TYR C 182 
 ARG   0.008   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  486)
  hydrogen bonds       : angle       4.58619 ( 1434)
  SS BOND              : bond        0.00189 (    4)
  SS BOND              : angle       2.07697 (    8)
  covalent geometry    : bond        0.00354 ( 7846)
  covalent geometry    : angle       0.75317 (10652)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 230
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  203 ASN cc_start: 0.8489 (t0) cc_final: 0.8238 (t0)
REVERT: A  233 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8092 (tm-30)
REVERT: A  255 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.7024 (t-90)
REVERT: A  282 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7978 (tpp)
REVERT: A  323 LEU cc_start: 0.8902 (mm) cc_final: 0.8684 (tp)
REVERT: A  334 ARG cc_start: 0.6798 (tmt170) cc_final: 0.5643 (ttm170)
REVERT: B  139 GLN cc_start: 0.8205 (mt0) cc_final: 0.8003 (mt0)
REVERT: B  149 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6855 (p90)
REVERT: C  140 MET cc_start: 0.8575 (tpp) cc_final: 0.8373 (tpp)
REVERT: C  177 MET cc_start: 0.7767 (tpp) cc_final: 0.6985 (tpp)
REVERT: C  248 ASP cc_start: 0.8094 (t0) cc_final: 0.7858 (t0)
REVERT: C  250 ASN cc_start: 0.7625 (p0) cc_final: 0.7156 (t0)
REVERT: C  251 GLU cc_start: 0.7362 (pm20) cc_final: 0.6928 (pm20)
REVERT: C  332 GLN cc_start: 0.8482 (mt0) cc_final: 0.8265 (mt0)
REVERT: C  334 ARG cc_start: 0.6719 (tmt170) cc_final: 0.5649 (ttt180)
REVERT: D  149 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.6860 (p90)
  outliers start: 42
  outliers final: 38
  residues processed: 252
  average time/residue: 0.1547
  time to fit residues: 55.1097
Evaluate side-chains
  269 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 227
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  255 HIS
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain B residue   27 CYS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   53 CYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  126 VAL
Chi-restraints excluded: chain D residue  147 ILE
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 65 optimal weight:    0.0270
   chunk 64 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** D  52 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 = 0.3738 r_free = 0.3738 target = 0.122795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.101279 restraints weight = 17955.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.103085 restraints weight = 10925.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.104034 restraints weight = 8511.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7850  Z= 0.146
  Angle     :  0.749  10.188  10660  Z= 0.382
  Chirality :  0.044   0.182   1138
  Planarity :  0.006   0.057   1296
  Dihedral  :  7.007  59.971   1070
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 31.14 %
    Favored  : 63.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.28), residues: 886
  helix:  1.18 (0.22), residues: 562
  sheet: -0.46 (0.66), residues: 56
  loop : -3.33 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  84 
 HIS   0.005   0.001   HIS D 117 
 PHE   0.016   0.001   PHE C 271 
 TYR   0.024   0.001   TYR D  92 
 ARG   0.007   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04181 (  486)
  hydrogen bonds       : angle       4.56486 ( 1434)
  SS BOND              : bond        0.00178 (    4)
  SS BOND              : angle       2.02048 (    8)
  covalent geometry    : bond        0.00331 ( 7846)
  covalent geometry    : angle       0.74718 (10652)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2566.75 seconds
wall clock time: 45 minutes 50.22 seconds (2750.22 seconds total)