Starting phenix.real_space_refine
on Wed Mar 12 12:26:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8izf_35863/03_2025/8izf_35863.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8izf_35863/03_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_35863/03_2025/8izf_35863.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8izf_35863/03_2025/8izf_35863.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8izf_35863/03_2025/8izf_35863.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8izf_35863/03_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-5624/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: 5.98, per 1000 atoms: 0.79
  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: 2.15
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.68
  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: 1.95

  Time building geometry restraints manager: 2.48 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: 0.04
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:             1.220
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.270
  Find NCS groups from input model:        0.140
  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:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.130
-------------------------------------------------------------------------------
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   7846  Z= 0.383
  Angle     :  1.095  19.322  10652  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 

*********************** 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  : 0.859 
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: 0.1741
  time to fit residues: 72.7074
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  : 0.818 
-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.132011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.109595 restraints weight = 16754.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.112720 restraints weight = 9748.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.114831 restraints weight = 6834.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
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   7846  Z= 0.215
  Angle     :  0.723  13.409  10652  Z= 0.372
  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 

*********************** 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  : 0.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8439 (p-90) cc_final: 0.8052 (p-90)
REVERT: A  140 MET cc_start: 0.8496 (tpp) cc_final: 0.7820 (tpp)
REVERT: A  168 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6607 (m90)
REVERT: A  203 ASN cc_start: 0.8562 (t0) cc_final: 0.8330 (t0)
REVERT: A  233 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8413 (tt0)
REVERT: A  332 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7787 (mt0)
REVERT: A  334 ARG cc_start: 0.6468 (tmt170) cc_final: 0.5639 (ttt180)
REVERT: A  343 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7895 (t80)
REVERT: A  357 VAL cc_start: 0.7659 (t) cc_final: 0.7454 (p)
REVERT: A  370 TYR cc_start: 0.8082 (t80) cc_final: 0.7841 (t80)
REVERT: B   80 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7002 (tt0)
REVERT: B  148 TYR cc_start: 0.7963 (m-80) cc_final: 0.7643 (m-80)
REVERT: C   84 TRP cc_start: 0.8425 (p-90) cc_final: 0.8040 (p-90)
REVERT: C  168 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.6575 (m90)
REVERT: C  203 ASN cc_start: 0.8723 (t0) cc_final: 0.8488 (t0)
REVERT: C  332 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7738 (mt0)
REVERT: C  334 ARG cc_start: 0.6497 (tmt170) cc_final: 0.5676 (ttt180)
REVERT: C  343 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7905 (t80)
REVERT: C  370 TYR cc_start: 0.8073 (t80) cc_final: 0.7759 (t80)
REVERT: D   65 ILE cc_start: 0.9311 (pt) cc_final: 0.9087 (pt)
REVERT: D   80 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7081 (mt-10)
  outliers start: 35
  outliers final: 23
  residues processed: 266
  average time/residue: 0.1575
  time to fit residues: 59.0434
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  : 0.814 
-------------------------------------------------------------------------------
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:    3.9990
   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:    3.3990

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.124868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.103354 restraints weight = 17352.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.105490 restraints weight = 10010.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.106384 restraints weight = 7801.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076   7846  Z= 0.478
  Angle     :  0.834  12.881  10652  Z= 0.432
  Chirality :  0.048   0.200   1138
  Planarity :  0.006   0.057   1296
  Dihedral  :  9.578  59.901   1082
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 18.73 %
    Favored  : 73.57 %
  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: -1.10 (0.28), residues: 886
  helix:  0.69 (0.21), residues: 556
  sheet: -1.35 (0.58), residues: 56
  loop : -3.68 (0.33), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP C  72 
 HIS   0.011   0.002   HIS A  82 
 PHE   0.027   0.002   PHE A 158 
 TYR   0.039   0.003   TYR C 279 
 ARG   0.005   0.001   ARG C  76 

*********************** 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
  270 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 208
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.8655 (tpp) cc_final: 0.8391 (tpp)
REVERT: A  168 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.6733 (m90)
REVERT: A  203 ASN cc_start: 0.8802 (t0) cc_final: 0.8574 (t0)
REVERT: A  224 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.6974 (t80)
REVERT: A  233 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8033 (tm-30)
REVERT: A  248 ASP cc_start: 0.7720 (t70) cc_final: 0.6892 (t0)
REVERT: A  332 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7887 (mt0)
REVERT: A  334 ARG cc_start: 0.6808 (tmt170) cc_final: 0.5911 (ttt180)
REVERT: A  343 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7835 (t80)
REVERT: B   38 GLU cc_start: 0.8340 (tp30) cc_final: 0.8023 (tp30)
REVERT: B   67 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8999 (tt)
REVERT: B  149 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7489 (p90)
REVERT: C  168 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.6739 (m90)
REVERT: C  203 ASN cc_start: 0.8800 (t0) cc_final: 0.8575 (t0)
REVERT: C  224 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.6958 (t80)
REVERT: C  289 LEU cc_start: 0.8971 (tp) cc_final: 0.8701 (tt)
REVERT: C  332 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7927 (mt0)
REVERT: C  334 ARG cc_start: 0.6803 (tmt170) cc_final: 0.5905 (ttt180)
REVERT: C  343 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7907 (t80)
REVERT: D   38 GLU cc_start: 0.8237 (tp30) cc_final: 0.7920 (tp30)
REVERT: D  144 ASP cc_start: 0.7890 (t0) cc_final: 0.7646 (t0)
REVERT: D  149 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.7417 (p90)
  outliers start: 62
  outliers final: 43
  residues processed: 247
  average time/residue: 0.1491
  time to fit residues: 52.6784
Evaluate side-chains
  262 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 208
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
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  185 VAL
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  185 VAL
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  149 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.119277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.097538 restraints weight = 17857.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.099382 restraints weight = 10880.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.100345 restraints weight = 8466.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7846  Z= 0.237
  Angle     :  0.709  11.771  10652  Z= 0.363
  Chirality :  0.043   0.188   1138
  Planarity :  0.005   0.054   1296
  Dihedral  :  8.753  59.061   1082
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  6.95 %
    Allowed  : 23.08 %
    Favored  : 69.98 %
  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: -0.91 (0.28), residues: 886
  helix:  0.88 (0.21), residues: 552
  sheet: -0.68 (0.59), 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   0.011   0.001   HIS A  82 
 PHE   0.027   0.002   PHE A 158 
 TYR   0.025   0.002   TYR C 182 
 ARG   0.003   0.000   ARG B  90 

*********************** 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: 56
    poor density    : 234
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.8549 (tpp) cc_final: 0.8239 (tpp)
REVERT: A  168 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.6745 (m90)
REVERT: A  203 ASN cc_start: 0.8741 (t0) cc_final: 0.8437 (t0)
REVERT: A  224 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.6808 (t80)
REVERT: A  233 GLN cc_start: 0.8904 (tm-30) cc_final: 0.7951 (tm-30)
REVERT: A  248 ASP cc_start: 0.7472 (t70) cc_final: 0.6967 (t0)
REVERT: A  251 GLU cc_start: 0.7554 (pm20) cc_final: 0.7317 (pm20)
REVERT: A  334 ARG cc_start: 0.6928 (tmt170) cc_final: 0.5903 (ttt180)
REVERT: A  343 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7854 (t80)
REVERT: A  346 GLN cc_start: 0.8747 (mp10) cc_final: 0.8529 (mp10)
REVERT: B   38 GLU cc_start: 0.8213 (tp30) cc_final: 0.7849 (tp30)
REVERT: C  168 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.6758 (m90)
REVERT: C  203 ASN cc_start: 0.8754 (t0) cc_final: 0.8466 (t0)
REVERT: C  224 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.6931 (t80)
REVERT: C  248 ASP cc_start: 0.7571 (t0) cc_final: 0.7062 (t0)
REVERT: C  251 GLU cc_start: 0.7587 (pm20) cc_final: 0.7380 (pm20)
REVERT: C  334 ARG cc_start: 0.6798 (tmt170) cc_final: 0.5824 (ttt180)
REVERT: C  343 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7882 (t80)
REVERT: D   38 GLU cc_start: 0.8221 (tp30) cc_final: 0.7881 (tp30)
REVERT: D   92 TYR cc_start: 0.8748 (m-10) cc_final: 0.8462 (m-10)
  outliers start: 56
  outliers final: 39
  residues processed: 267
  average time/residue: 0.1515
  time to fit residues: 57.4417
Evaluate side-chains
  256 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 211
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
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  225 LEU
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  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  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  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   27 CYS
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:    0.9980
   chunk 71 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.120924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.098915 restraints weight = 17612.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.100618 restraints weight = 10864.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.101597 restraints weight = 8599.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7846  Z= 0.209
  Angle     :  0.684  11.105  10652  Z= 0.348
  Chirality :  0.043   0.181   1138
  Planarity :  0.005   0.052   1296
  Dihedral  :  8.323  59.190   1082
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  7.57 %
    Allowed  : 25.06 %
    Favored  : 67.37 %
  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: -0.79 (0.28), residues: 886
  helix:  0.98 (0.21), residues: 552
  sheet: -0.86 (0.59), residues: 56
  loop : -3.71 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  84 
 HIS   0.003   0.001   HIS B 113 
 PHE   0.027   0.001   PHE A 158 
 TYR   0.020   0.002   TYR D  42 
 ARG   0.005   0.000   ARG D  70 

*********************** 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
  288 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 227
  time to evaluate  : 0.952 
Fit side-chains
REVERT: A  203 ASN cc_start: 0.8581 (t0) cc_final: 0.8284 (t0)
REVERT: A  224 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.7016 (t80)
REVERT: A  233 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8215 (tm-30)
REVERT: A  248 ASP cc_start: 0.7413 (t70) cc_final: 0.6684 (t0)
REVERT: A  251 GLU cc_start: 0.7376 (pm20) cc_final: 0.6975 (pm20)
REVERT: A  255 HIS cc_start: 0.7428 (OUTLIER) cc_final: 0.6176 (t-90)
REVERT: A  332 GLN cc_start: 0.8464 (mt0) cc_final: 0.7579 (mt0)
REVERT: A  334 ARG cc_start: 0.6903 (tmt170) cc_final: 0.5860 (ttt180)
REVERT: B   38 GLU cc_start: 0.8231 (tp30) cc_final: 0.7914 (tp30)
REVERT: B  147 ILE cc_start: 0.9512 (tp) cc_final: 0.9312 (tp)
REVERT: B  149 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7408 (p90)
REVERT: C  203 ASN cc_start: 0.8630 (t0) cc_final: 0.8322 (t0)
REVERT: C  224 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7095 (t80)
REVERT: C  248 ASP cc_start: 0.7527 (t0) cc_final: 0.6721 (t0)
REVERT: C  251 GLU cc_start: 0.7433 (pm20) cc_final: 0.7085 (pm20)
REVERT: C  332 GLN cc_start: 0.8485 (mt0) cc_final: 0.8255 (mt0)
REVERT: C  334 ARG cc_start: 0.6875 (tmt170) cc_final: 0.5801 (ttt180)
REVERT: D   38 GLU cc_start: 0.8227 (tp30) cc_final: 0.7917 (tp30)
REVERT: D  149 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7383 (p90)
  outliers start: 61
  outliers final: 37
  residues processed: 264
  average time/residue: 0.1527
  time to fit residues: 57.7922
Evaluate side-chains
  258 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 216
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
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  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  330 LEU
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  126 VAL
Chi-restraints excluded: chain B residue  149 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   64 VAL
Chi-restraints excluded: chain D residue  126 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:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.121177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.099351 restraints weight = 17502.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.101167 restraints weight = 10595.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.102069 restraints weight = 8330.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7846  Z= 0.234
  Angle     :  0.715  11.234  10652  Z= 0.365
  Chirality :  0.043   0.168   1138
  Planarity :  0.005   0.051   1296
  Dihedral  :  7.572  57.378   1074
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 26.05 %
    Favored  : 66.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.74 (0.28), residues: 886
  helix:  0.91 (0.21), residues: 560
  sheet: -0.81 (0.57), residues: 56
  loop : -3.55 (0.33), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  84 
 HIS   0.003   0.001   HIS C 256 
 PHE   0.035   0.002   PHE C 158 
 TYR   0.019   0.002   TYR D  42 
 ARG   0.004   0.000   ARG D  70 

*********************** 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
  290 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 232
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8420 (p-90) cc_final: 0.8200 (p-90)
REVERT: A  203 ASN cc_start: 0.8590 (t0) cc_final: 0.8304 (t0)
REVERT: A  224 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7194 (t80)
REVERT: A  233 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8730 (tm-30)
REVERT: A  248 ASP cc_start: 0.7521 (t70) cc_final: 0.6712 (t0)
REVERT: A  251 GLU cc_start: 0.7306 (pm20) cc_final: 0.6894 (pm20)
REVERT: A  255 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.5996 (t-90)
REVERT: A  334 ARG cc_start: 0.6833 (tmt170) cc_final: 0.5794 (ttt180)
REVERT: B  149 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.7417 (p90)
REVERT: C  140 MET cc_start: 0.8767 (tpp) cc_final: 0.8306 (tpp)
REVERT: C  203 ASN cc_start: 0.8612 (t0) cc_final: 0.8293 (t0)
REVERT: C  224 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7147 (t80)
REVERT: C  248 ASP cc_start: 0.7516 (t0) cc_final: 0.6679 (t0)
REVERT: C  251 GLU cc_start: 0.7309 (pm20) cc_final: 0.6900 (pm20)
REVERT: C  255 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.6660 (t-90)
REVERT: C  334 ARG cc_start: 0.6832 (tmt170) cc_final: 0.5776 (ttt180)
REVERT: D  149 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7367 (p90)
  outliers start: 58
  outliers final: 44
  residues processed: 267
  average time/residue: 0.1821
  time to fit residues: 68.4713
Evaluate side-chains
  267 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 217
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
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  224 TYR
Chi-restraints excluded: chain A residue  225 LEU
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  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  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  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  193 CYS
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  255 HIS
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  323 LEU
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   67 LEU
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:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0470
   chunk 7 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0870
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.4256

-------------------------------------------------------------------------------
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**
** 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 = 0.3747 r_free = 0.3747 target = 0.123538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.101351 restraints weight = 17618.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.104043 restraints weight = 10252.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.105327 restraints weight = 7123.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7846  Z= 0.195
  Angle     :  0.697   9.635  10652  Z= 0.357
  Chirality :  0.043   0.161   1138
  Planarity :  0.005   0.050   1296
  Dihedral  :  7.363  56.502   1074
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 28.29 %
    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: -0.61 (0.28), residues: 886
  helix:  1.02 (0.21), residues: 558
  sheet: -0.58 (0.58), residues: 56
  loop : -3.52 (0.32), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  84 
 HIS   0.003   0.001   HIS D 113 
 PHE   0.035   0.002   PHE C 158 
 TYR   0.021   0.001   TYR D  42 
 ARG   0.004   0.000   ARG D  70 

*********************** 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
  285 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 244
  time to evaluate  : 0.914 
Fit side-chains
REVERT: A   84 TRP cc_start: 0.8421 (p-90) cc_final: 0.8185 (p-90)
REVERT: A  203 ASN cc_start: 0.8518 (t0) cc_final: 0.8172 (t0)
REVERT: A  224 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7295 (t80)
REVERT: A  233 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8032 (tm-30)
REVERT: A  334 ARG cc_start: 0.6851 (tmt170) cc_final: 0.5777 (ttt180)
REVERT: B   44 THR cc_start: 0.9400 (t) cc_final: 0.9174 (t)
REVERT: B  118 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: B  139 GLN cc_start: 0.8157 (mt0) cc_final: 0.7935 (mt0)
REVERT: B  149 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7368 (p90)
REVERT: C   84 TRP cc_start: 0.8368 (p-90) cc_final: 0.8097 (p-90)
REVERT: C   91 LEU cc_start: 0.8215 (pp) cc_final: 0.7970 (pp)
REVERT: C  203 ASN cc_start: 0.8491 (t0) cc_final: 0.8259 (t0)
REVERT: C  224 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.6974 (t80)
REVERT: C  233 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8139 (tt0)
REVERT: C  323 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8803 (tp)
REVERT: C  332 GLN cc_start: 0.8493 (mt0) cc_final: 0.8237 (mt0)
REVERT: C  334 ARG cc_start: 0.6810 (tmt170) cc_final: 0.5697 (ttt180)
REVERT: D   44 THR cc_start: 0.9391 (t) cc_final: 0.9172 (t)
REVERT: D  149 HIS cc_start: 0.7605 (OUTLIER) cc_final: 0.7121 (p90)
  outliers start: 41
  outliers final: 26
  residues processed: 263
  average time/residue: 0.2345
  time to fit residues: 88.1554
Evaluate side-chains
  260 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 229
  time to evaluate  : 1.710 
-------------------------------------------------------------------------------
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  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  268 VAL
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  113 PHE
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  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   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:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.130840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.108252 restraints weight = 17311.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.111166 restraints weight = 10438.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.113009 restraints weight = 7533.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.4618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7846  Z= 0.212
  Angle     :  0.718  10.149  10652  Z= 0.365
  Chirality :  0.044   0.174   1138
  Planarity :  0.005   0.050   1296
  Dihedral  :  7.218  56.120   1072
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 30.52 %
    Favored  : 64.52 %
  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: -0.53 (0.28), residues: 886
  helix:  1.02 (0.21), residues: 562
  sheet: -0.71 (0.60), residues: 56
  loop : -3.38 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  68 
 HIS   0.004   0.001   HIS A 319 
 PHE   0.033   0.001   PHE C 158 
 TYR   0.028   0.002   TYR C 182 
 ARG   0.003   0.000   ARG D  70 

*********************** 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
  274 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 234
  time to evaluate  : 0.859 
Fit side-chains
REVERT: A   84 TRP cc_start: 0.8319 (p-90) cc_final: 0.8103 (p-90)
REVERT: A  140 MET cc_start: 0.8743 (tpp) cc_final: 0.8315 (tpp)
REVERT: A  203 ASN cc_start: 0.8222 (t0) cc_final: 0.8014 (t0)
REVERT: A  233 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8044 (tm-30)
REVERT: A  248 ASP cc_start: 0.7838 (t0) cc_final: 0.6736 (t0)
REVERT: A  251 GLU cc_start: 0.7422 (pm20) cc_final: 0.6867 (pm20)
REVERT: A  255 HIS cc_start: 0.7308 (OUTLIER) cc_final: 0.6557 (t-90)
REVERT: A  334 ARG cc_start: 0.6604 (tmt170) cc_final: 0.5639 (ttt180)
REVERT: B  149 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.7035 (p90)
REVERT: C   91 LEU cc_start: 0.8322 (pp) cc_final: 0.8082 (pp)
REVERT: C  248 ASP cc_start: 0.7795 (t0) cc_final: 0.6806 (t0)
REVERT: C  251 GLU cc_start: 0.7460 (pm20) cc_final: 0.7083 (pm20)
REVERT: C  323 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8607 (tp)
REVERT: C  334 ARG cc_start: 0.6598 (tmt170) cc_final: 0.5585 (ttt180)
REVERT: D  149 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6919 (p90)
  outliers start: 40
  outliers final: 31
  residues processed: 253
  average time/residue: 0.1570
  time to fit residues: 56.2111
Evaluate side-chains
  253 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 218
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
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  225 LEU
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  255 HIS
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   44 THR
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  137 LEU
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue  113 PHE
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  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:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 13 optimal weight:    0.4980
   chunk 43 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3915 r_free = 0.3915 target = 0.133017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.110020 restraints weight = 17478.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.113219 restraints weight = 10094.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.115402 restraints weight = 7064.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.4767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7846  Z= 0.219
  Angle     :  0.740   9.990  10652  Z= 0.378
  Chirality :  0.044   0.165   1138
  Planarity :  0.005   0.054   1296
  Dihedral  :  7.081  56.468   1070
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 30.77 %
    Favored  : 64.02 %
  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: -0.44 (0.28), residues: 886
  helix:  1.05 (0.21), residues: 564
  sheet: -0.64 (0.61), residues: 56
  loop : -3.28 (0.33), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  68 
 HIS   0.002   0.001   HIS D 113 
 PHE   0.033   0.002   PHE B  24 
 TYR   0.019   0.001   TYR D  42 
 ARG   0.007   0.001   ARG C 156 

*********************** 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
  270 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 228
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8394 (p-90) cc_final: 0.8163 (p-90)
REVERT: A  140 MET cc_start: 0.8728 (tpp) cc_final: 0.8281 (tpp)
REVERT: A  203 ASN cc_start: 0.8384 (t0) cc_final: 0.8142 (t0)
REVERT: A  233 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8078 (tm-30)
REVERT: A  334 ARG cc_start: 0.6685 (tmt170) cc_final: 0.5672 (ttt180)
REVERT: B   97 GLU cc_start: 0.8023 (tt0) cc_final: 0.7819 (tt0)
REVERT: B  149 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7028 (p90)
REVERT: C   91 LEU cc_start: 0.8446 (pp) cc_final: 0.8214 (pp)
REVERT: C  140 MET cc_start: 0.8691 (tpp) cc_final: 0.8423 (tpp)
REVERT: C  323 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8701 (tp)
REVERT: C  334 ARG cc_start: 0.6672 (tmt170) cc_final: 0.5619 (ttt180)
REVERT: D  118 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7777 (tm-30)
REVERT: D  149 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6798 (p90)
  outliers start: 42
  outliers final: 33
  residues processed: 247
  average time/residue: 0.1538
  time to fit residues: 53.7833
Evaluate side-chains
  261 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 225
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
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  225 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  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   44 THR
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  137 LEU
Chi-restraints excluded: chain B residue  149 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  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  323 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 87 optimal weight:    7.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.122119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.100115 restraints weight = 18001.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.102849 restraints weight = 10408.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.104139 restraints weight = 7150.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.4843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7846  Z= 0.224
  Angle     :  0.746  10.242  10652  Z= 0.381
  Chirality :  0.045   0.174   1138
  Planarity :  0.006   0.055   1296
  Dihedral  :  7.066  57.056   1070
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 30.65 %
    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: -0.39 (0.28), residues: 886
  helix:  1.10 (0.21), residues: 562
  sheet: -0.62 (0.62), residues: 56
  loop : -3.26 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  68 
 HIS   0.002   0.001   HIS A 256 
 PHE   0.030   0.001   PHE C 158 
 TYR   0.034   0.002   TYR C 182 
 ARG   0.006   0.001   ARG C 156 

********************** 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
  270 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 228
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8423 (p-90) cc_final: 0.8160 (p-90)
REVERT: A  140 MET cc_start: 0.8728 (tpp) cc_final: 0.8292 (tpp)
REVERT: A  203 ASN cc_start: 0.8562 (t0) cc_final: 0.8281 (t0)
REVERT: A  233 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8084 (tm-30)
REVERT: A  251 GLU cc_start: 0.7446 (pm20) cc_final: 0.6891 (pm20)
REVERT: A  334 ARG cc_start: 0.6813 (tmt170) cc_final: 0.5635 (ttm170)
REVERT: B  149 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.6979 (p90)
REVERT: C   84 TRP cc_start: 0.8353 (p-90) cc_final: 0.7833 (p90)
REVERT: C   91 LEU cc_start: 0.8426 (pp) cc_final: 0.8191 (pp)
REVERT: C  140 MET cc_start: 0.8697 (tpp) cc_final: 0.8430 (tpp)
REVERT: C  334 ARG cc_start: 0.6760 (tmt170) cc_final: 0.5649 (ttt180)
REVERT: D  149 HIS cc_start: 0.7524 (OUTLIER) cc_final: 0.6819 (p90)
  outliers start: 42
  outliers final: 35
  residues processed: 247
  average time/residue: 0.1546
  time to fit residues: 53.7628
Evaluate side-chains
  259 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 222
  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  225 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  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   44 THR
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  137 LEU
Chi-restraints excluded: chain B residue  149 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  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 43 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0770
   chunk 83 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 64 optimal weight:    0.3980
   chunk 81 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
B  52 HIS
D  52 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.123987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.102265 restraints weight = 17845.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.104923 restraints weight = 10291.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.106651 restraints weight = 7099.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.5108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7846  Z= 0.204
  Angle     :  0.745  10.236  10652  Z= 0.382
  Chirality :  0.044   0.156   1138
  Planarity :  0.006   0.050   1296
  Dihedral  :  6.970  59.782   1070
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 31.89 %
    Favored  : 63.65 %
  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: -0.36 (0.28), residues: 886
  helix:  1.15 (0.21), residues: 562
  sheet: -0.58 (0.65), residues: 56
  loop : -3.29 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  68 
 HIS   0.003   0.001   HIS D 117 
 PHE   0.030   0.001   PHE A 373 
 TYR   0.034   0.001   TYR C 182 
 ARG   0.009   0.001   ARG D  45 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2659.15 seconds
wall clock time: 48 minutes 8.58 seconds (2888.58 seconds total)