Starting phenix.real_space_refine
on Wed Feb 12 12:01:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8izf_35863/02_2025/8izf_35863.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8izf_35863/02_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_35863/02_2025/8izf_35863.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8izf_35863/02_2025/8izf_35863.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8izf_35863/02_2025/8izf_35863.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8izf_35863/02_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-5592/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: 5.58, per 1000 atoms: 0.73
  Number of scatterers: 7594
  At special positions: 0
  Unit cell: (110.416, 101.84, 100.768, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       2     15.00
     O    1264      8.00
     N    1202      7.00
     C    5088      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, 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

  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: 2.02
  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: 0.57
  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: 2.23 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: 3953
       18.05 -    36.09: 410
       36.09 -    54.14: 98
       54.14 -    72.19: 16
       72.19 -    90.24: 15
  Dihedral angle restraints: 4492
    sinusoidal: 1828
      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 4489 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: 67
        2.54 -     3.13: 6465
        3.13 -     3.72: 12007
        3.72 -     4.31: 15506
        4.31 -     4.90: 25341
  Nonbonded interactions: 59386
  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=" SG  CYS D 102 "
            pdb=" SG  CYS D 142 "
     model   vdw
     2.029 3.760
  ... (remaining 59381 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:             1.040
  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:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.720
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.030
-------------------------------------------------------------------------------
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= 0.386
  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  : 0.873 
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: 0.1711
  time to fit residues: 71.7197
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  : 0.917 
-------------------------------------------------------------------------------
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 = 0.132166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.109793 restraints weight = 16749.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.112912 restraints weight = 9720.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.114927 restraints weight = 6784.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7846  Z= 0.216
  Angle     :  0.723  13.481  10652  Z= 0.372
  Chirality :  0.043   0.143   1138
  Planarity :  0.005   0.056   1296
  Dihedral  :  9.672  54.880   1084
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.48 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 16.63 %
    Favored  : 79.16 %
  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: -0.87 (0.28), residues: 886
  helix:  0.91 (0.21), residues: 546
  sheet: -1.67 (0.58), residues: 58
  loop : -3.44 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  68 
 HIS   0.005   0.001   HIS A  82 
 PHE   0.031   0.002   PHE A 158 
 TYR   0.031   0.002   TYR C 182 
 ARG   0.003   0.001   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
  286 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 252
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 TRP cc_start: 0.8436 (p-90) cc_final: 0.8047 (p-90)
REVERT: A  140 MET cc_start: 0.8476 (tpp) cc_final: 0.7806 (tpp)
REVERT: A  168 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.6618 (m90)
REVERT: A  203 ASN cc_start: 0.8580 (t0) cc_final: 0.8349 (t0)
REVERT: A  233 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8392 (tt0)
REVERT: A  332 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7780 (mt0)
REVERT: A  334 ARG cc_start: 0.6466 (tmt170) cc_final: 0.5635 (ttt180)
REVERT: A  343 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7871 (t80)
REVERT: A  357 VAL cc_start: 0.7686 (t) cc_final: 0.7476 (p)
REVERT: A  365 GLN cc_start: 0.8402 (tp40) cc_final: 0.8197 (tp40)
REVERT: A  370 TYR cc_start: 0.8089 (t80) cc_final: 0.7840 (t80)
REVERT: B   80 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6990 (tt0)
REVERT: B  148 TYR cc_start: 0.7953 (m-80) cc_final: 0.7629 (m-80)
REVERT: C   84 TRP cc_start: 0.8430 (p-90) cc_final: 0.8049 (p-90)
REVERT: C  168 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.6579 (m90)
REVERT: C  203 ASN cc_start: 0.8714 (t0) cc_final: 0.8477 (t0)
REVERT: C  332 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7749 (mt0)
REVERT: C  334 ARG cc_start: 0.6496 (tmt170) cc_final: 0.5669 (ttt180)
REVERT: C  343 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7917 (t80)
REVERT: C  370 TYR cc_start: 0.8075 (t80) cc_final: 0.7759 (t80)
REVERT: D   65 ILE cc_start: 0.9294 (pt) cc_final: 0.9084 (pt)
REVERT: D   80 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7080 (tt0)
REVERT: D  148 TYR cc_start: 0.7983 (m-80) cc_final: 0.7689 (m-80)
REVERT: D  150 MET cc_start: 0.7625 (ttp) cc_final: 0.7093 (ptm)
  outliers start: 34
  outliers final: 23
  residues processed: 268
  average time/residue: 0.1533
  time to fit residues: 57.9817
Evaluate side-chains
  239 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 210
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 86 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 76 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.8386

-------------------------------------------------------------------------------
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 = 0.3854 r_free = 0.3854 target = 0.128858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.107303 restraints weight = 17122.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.109729 restraints weight = 9767.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.111314 restraints weight = 6739.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7846  Z= 0.301
  Angle     :  0.726  11.307  10652  Z= 0.377
  Chirality :  0.044   0.219   1138
  Planarity :  0.005   0.055   1296
  Dihedral  :  9.197  57.079   1082
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 19.35 %
    Favored  : 74.81 %
  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: -0.86 (0.28), residues: 886
  helix:  0.90 (0.21), residues: 552
  sheet: -1.15 (0.60), residues: 56
  loop : -3.59 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP C  72 
 HIS   0.007   0.002   HIS C  82 
 PHE   0.026   0.002   PHE A 158 
 TYR   0.027   0.002   TYR A 279 
 ARG   0.004   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
  275 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 228
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.8540 (tpp) cc_final: 0.8250 (tpp)
REVERT: A  168 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.6830 (m90)
REVERT: A  203 ASN cc_start: 0.8682 (t0) cc_final: 0.8443 (t0)
REVERT: A  224 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.6965 (t80)
REVERT: A  233 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8018 (tm-30)
REVERT: A  248 ASP cc_start: 0.7627 (t70) cc_final: 0.6828 (t0)
REVERT: A  334 ARG cc_start: 0.6651 (tmt170) cc_final: 0.5758 (ttt180)
REVERT: A  343 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7857 (t80)
REVERT: B   67 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8976 (tt)
REVERT: B   80 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7172 (tt0)
REVERT: C  168 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.6834 (m90)
REVERT: C  203 ASN cc_start: 0.8673 (t0) cc_final: 0.8435 (t0)
REVERT: C  224 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7106 (t80)
REVERT: C  248 ASP cc_start: 0.7693 (t0) cc_final: 0.7029 (t0)
REVERT: C  334 ARG cc_start: 0.6647 (tmt170) cc_final: 0.5775 (ttt180)
REVERT: C  343 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7894 (t80)
REVERT: D   80 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7281 (mt-10)
REVERT: D   92 TYR cc_start: 0.8731 (m-10) cc_final: 0.8288 (m-10)
REVERT: D  140 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8550 (tm-30)
  outliers start: 47
  outliers final: 30
  residues processed: 257
  average time/residue: 0.1606
  time to fit residues: 58.4014
Evaluate side-chains
  237 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 200
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
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  194 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  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   67 LEU
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  168 HIS
Chi-restraints excluded: chain C residue  175 GLU
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain C residue  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 26 optimal weight:    9.9990
   chunk 68 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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**
B 113 HIS
** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 113 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.118221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.096061 restraints weight = 17872.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.097628 restraints weight = 11043.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.098554 restraints weight = 8873.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7846  Z= 0.318
  Angle     :  0.732  11.657  10652  Z= 0.376
  Chirality :  0.045   0.207   1138
  Planarity :  0.005   0.054   1296
  Dihedral  :  8.798  59.309   1082
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  7.94 %
    Allowed  : 21.84 %
    Favored  : 70.22 %
  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: -0.89 (0.28), residues: 886
  helix:  0.90 (0.21), residues: 552
  sheet: -0.94 (0.60), residues: 56
  loop : -3.71 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  72 
 HIS   0.008   0.001   HIS A 319 
 PHE   0.031   0.002   PHE C 158 
 TYR   0.022   0.002   TYR C 182 
 ARG   0.005   0.001   ARG D  70 

*********************** 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
  287 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 223
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.6838 (m90)
REVERT: A  203 ASN cc_start: 0.8759 (t0) cc_final: 0.8434 (t0)
REVERT: A  224 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.6809 (t80)
REVERT: A  233 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8144 (tm-30)
REVERT: A  248 ASP cc_start: 0.7546 (t70) cc_final: 0.7012 (t0)
REVERT: A  251 GLU cc_start: 0.7633 (pm20) cc_final: 0.7387 (pm20)
REVERT: A  332 GLN cc_start: 0.8486 (mt0) cc_final: 0.7676 (mt0)
REVERT: A  334 ARG cc_start: 0.6944 (tmt170) cc_final: 0.5918 (ttt180)
REVERT: A  343 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7805 (t80)
REVERT: A  346 GLN cc_start: 0.8864 (mp10) cc_final: 0.8562 (mp10)
REVERT: B   38 GLU cc_start: 0.8275 (tp30) cc_final: 0.7951 (tp30)
REVERT: B   93 GLU cc_start: 0.8261 (tm-30) cc_final: 0.8054 (tm-30)
REVERT: B  149 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.7453 (p90)
REVERT: C  140 MET cc_start: 0.8837 (tpp) cc_final: 0.8589 (tpp)
REVERT: C  168 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.6829 (m90)
REVERT: C  203 ASN cc_start: 0.8778 (t0) cc_final: 0.8488 (t0)
REVERT: C  224 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.6811 (t80)
REVERT: C  248 ASP cc_start: 0.7658 (t0) cc_final: 0.6829 (t0)
REVERT: C  251 GLU cc_start: 0.7682 (pm20) cc_final: 0.7451 (pm20)
REVERT: C  332 GLN cc_start: 0.8535 (mt0) cc_final: 0.7667 (mt0)
REVERT: C  334 ARG cc_start: 0.6903 (tmt170) cc_final: 0.5892 (ttt180)
REVERT: C  343 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7846 (t80)
REVERT: C  346 GLN cc_start: 0.8872 (mp10) cc_final: 0.8622 (mp10)
REVERT: D   38 GLU cc_start: 0.8265 (tp30) cc_final: 0.7970 (tp30)
REVERT: D   80 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7294 (mt-10)
REVERT: D  140 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8719 (tm-30)
REVERT: D  149 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7486 (p90)
  outliers start: 64
  outliers final: 47
  residues processed: 262
  average time/residue: 0.1448
  time to fit residues: 54.4524
Evaluate side-chains
  257 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 202
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
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  193 CYS
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  236 CYS
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  325 ILE
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   53 CYS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  144 THR
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  325 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 60 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.121255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.099577 restraints weight = 17420.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.101370 restraints weight = 10689.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.102307 restraints weight = 8363.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7846  Z= 0.208
  Angle     :  0.672  10.423  10652  Z= 0.344
  Chirality :  0.042   0.188   1138
  Planarity :  0.005   0.052   1296
  Dihedral  :  8.297  59.448   1082
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 24.32 %
    Favored  : 68.49 %
  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: -0.71 (0.28), residues: 886
  helix:  1.07 (0.21), residues: 552
  sheet: -0.88 (0.61), residues: 56
  loop : -3.73 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  68 
 HIS   0.005   0.001   HIS A 319 
 PHE   0.029   0.002   PHE C 158 
 TYR   0.020   0.002   TYR D  42 
 ARG   0.003   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: 58
    poor density    : 230
  time to evaluate  : 0.835 
Fit side-chains
REVERT: A  203 ASN cc_start: 0.8602 (t0) cc_final: 0.8302 (t0)
REVERT: A  224 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7004 (t80)
REVERT: A  233 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: A  248 ASP cc_start: 0.7489 (t70) cc_final: 0.6767 (t0)
REVERT: A  251 GLU cc_start: 0.7430 (pm20) cc_final: 0.7042 (pm20)
REVERT: A  255 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6790 (t-90)
REVERT: A  332 GLN cc_start: 0.8427 (mt0) cc_final: 0.8071 (mt0)
REVERT: A  334 ARG cc_start: 0.6843 (tmt170) cc_final: 0.5776 (ttt180)
REVERT: A  346 GLN cc_start: 0.8729 (mp10) cc_final: 0.8447 (mp10)
REVERT: B   38 GLU cc_start: 0.8214 (tp30) cc_final: 0.7911 (tp30)
REVERT: B   93 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7777 (tm-30)
REVERT: B  149 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7398 (p90)
REVERT: C  203 ASN cc_start: 0.8578 (t0) cc_final: 0.8231 (t0)
REVERT: C  224 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7072 (t80)
REVERT: C  248 ASP cc_start: 0.7448 (t0) cc_final: 0.6637 (t0)
REVERT: C  251 GLU cc_start: 0.7464 (pm20) cc_final: 0.7127 (pm20)
REVERT: C  255 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.6790 (t-90)
REVERT: C  334 ARG cc_start: 0.6843 (tmt170) cc_final: 0.5791 (ttt180)
REVERT: C  343 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7859 (t80)
REVERT: C  346 GLN cc_start: 0.8762 (mp10) cc_final: 0.8556 (mp10)
REVERT: D   38 GLU cc_start: 0.8219 (tp30) cc_final: 0.7923 (tp30)
REVERT: D  149 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7436 (p90)
  outliers start: 58
  outliers final: 33
  residues processed: 264
  average time/residue: 0.1474
  time to fit residues: 55.6115
Evaluate side-chains
  258 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 218
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
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  252 LEU
Chi-restraints excluded: chain A residue  255 HIS
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  339 TYR
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  137 LEU
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  193 CYS
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  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
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   64 VAL
Chi-restraints excluded: chain D residue  100 SER
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:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 42 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3704 r_free = 0.3704 target = 0.120788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.098576 restraints weight = 17506.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.101037 restraints weight = 10352.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.102399 restraints weight = 7274.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.4160

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= 0.236
  Angle     :  0.701  11.170  10652  Z= 0.358
  Chirality :  0.043   0.169   1138
  Planarity :  0.005   0.051   1296
  Dihedral  :  7.745  58.570   1076
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.48 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 26.30 %
    Favored  : 67.49 %
  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:  0.98 (0.21), residues: 562
  sheet: -0.59 (0.63), residues: 56
  loop : -3.49 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  84 
 HIS   0.003   0.001   HIS A 319 
 PHE   0.035   0.002   PHE C 158 
 TYR   0.025   0.002   TYR C 182 
 ARG   0.004   0.000   ARG D  78 

*********************** 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
  277 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 227
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 ASN cc_start: 0.8588 (t0) cc_final: 0.8285 (t0)
REVERT: A  224 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7030 (t80)
REVERT: A  233 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8673 (tm-30)
REVERT: A  255 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.6780 (t-90)
REVERT: A  334 ARG cc_start: 0.6852 (tmt170) cc_final: 0.5758 (ttt180)
REVERT: A  346 GLN cc_start: 0.8842 (mp10) cc_final: 0.8536 (mp10)
REVERT: B   93 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7836 (tm-30)
REVERT: B  149 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7422 (p90)
REVERT: C  140 MET cc_start: 0.8738 (tpp) cc_final: 0.8278 (tpp)
REVERT: C  203 ASN cc_start: 0.8576 (t0) cc_final: 0.8303 (t0)
REVERT: C  224 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7213 (t80)
REVERT: C  248 ASP cc_start: 0.7522 (t0) cc_final: 0.6684 (t0)
REVERT: C  251 GLU cc_start: 0.7309 (pm20) cc_final: 0.6896 (pm20)
REVERT: C  255 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.6708 (t-90)
REVERT: C  334 ARG cc_start: 0.6823 (tmt170) cc_final: 0.5754 (ttt180)
REVERT: C  346 GLN cc_start: 0.8867 (mp10) cc_final: 0.8607 (mp10)
REVERT: D   38 GLU cc_start: 0.8251 (tp30) cc_final: 0.7976 (tp30)
REVERT: D   77 LYS cc_start: 0.8803 (mttt) cc_final: 0.8545 (mmmm)
REVERT: D  149 HIS cc_start: 0.7805 (OUTLIER) cc_final: 0.7386 (p90)
  outliers start: 50
  outliers final: 39
  residues processed: 257
  average time/residue: 0.1609
  time to fit residues: 57.9293
Evaluate side-chains
  259 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 214
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 HIS
Chi-restraints excluded: chain A residue  113 PHE
Chi-restraints excluded: chain A residue  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  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  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  100 SER
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   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  255 HIS
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  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   64 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:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 83 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0070
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.122175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.100170 restraints weight = 17599.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.102930 restraints weight = 10292.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.104100 restraints weight = 7053.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.4438

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= 0.204
  Angle     :  0.696  10.138  10652  Z= 0.357
  Chirality :  0.043   0.166   1138
  Planarity :  0.005   0.050   1296
  Dihedral  :  7.417  56.702   1074
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 27.30 %
    Favored  : 67.49 %
  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: -0.52 (0.28), residues: 886
  helix:  1.02 (0.21), residues: 562
  sheet: -0.31 (0.67), residues: 56
  loop : -3.44 (0.33), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  84 
 HIS   0.003   0.001   HIS D  52 
 PHE   0.035   0.001   PHE C 158 
 TYR   0.020   0.001   TYR B  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
  286 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 244
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.8723 (tpp) cc_final: 0.8285 (tpp)
REVERT: A  203 ASN cc_start: 0.8548 (t0) cc_final: 0.8203 (t0)
REVERT: A  224 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7090 (t80)
REVERT: A  233 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: A  288 LEU cc_start: 0.8392 (mt) cc_final: 0.8147 (mt)
REVERT: A  323 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8681 (tp)
REVERT: A  334 ARG cc_start: 0.6811 (tmt170) cc_final: 0.5772 (ttt180)
REVERT: B   92 TYR cc_start: 0.8504 (m-10) cc_final: 0.8286 (m-10)
REVERT: B   93 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7804 (tm-30)
REVERT: B  118 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: B  139 GLN cc_start: 0.8153 (mt0) cc_final: 0.7923 (mt0)
REVERT: B  149 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.7370 (p90)
REVERT: C  203 ASN cc_start: 0.8505 (t0) cc_final: 0.8256 (t0)
REVERT: C  224 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7139 (t80)
REVERT: C  323 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8799 (tp)
REVERT: C  332 GLN cc_start: 0.8335 (mt0) cc_final: 0.7985 (mt0)
REVERT: C  334 ARG cc_start: 0.6843 (tmt170) cc_final: 0.5715 (ttt180)
REVERT: D  149 HIS cc_start: 0.7678 (OUTLIER) cc_final: 0.7105 (p90)
  outliers start: 42
  outliers final: 32
  residues processed: 267
  average time/residue: 0.1591
  time to fit residues: 59.5055
Evaluate side-chains
  269 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 231
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
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  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  263 ILE
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  364 LEU
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  147 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  219 LEU
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  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   64 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:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.9786

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.130837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.107602 restraints weight = 17101.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.110689 restraints weight = 9965.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.112764 restraints weight = 7063.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.4572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7846  Z= 0.226
  Angle     :  0.718  10.703  10652  Z= 0.364
  Chirality :  0.044   0.202   1138
  Planarity :  0.005   0.050   1296
  Dihedral  :  7.333  56.869   1074
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 27.42 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.28), residues: 886
  helix:  1.09 (0.21), residues: 560
  sheet: -0.50 (0.66), residues: 56
  loop : -3.36 (0.33), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  84 
 HIS   0.003   0.001   HIS C 319 
 PHE   0.028   0.002   PHE A 158 
 TYR   0.027   0.002   TYR C 182 
 ARG   0.003   0.000   ARG B  90 

*********************** 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
  282 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 236
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.8705 (tpp) cc_final: 0.8234 (tpp)
REVERT: A  203 ASN cc_start: 0.8409 (t0) cc_final: 0.8174 (t0)
REVERT: A  224 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7283 (t80)
REVERT: A  233 GLN cc_start: 0.8829 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: A  248 ASP cc_start: 0.7849 (t0) cc_final: 0.6676 (t0)
REVERT: A  251 GLU cc_start: 0.7452 (pm20) cc_final: 0.6962 (pm20)
REVERT: A  334 ARG cc_start: 0.6641 (tmt170) cc_final: 0.5640 (ttt180)
REVERT: B   93 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7858 (tm-30)
REVERT: B  149 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.7071 (p90)
REVERT: C  140 MET cc_start: 0.8681 (tpp) cc_final: 0.8394 (tpp)
REVERT: C  224 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7195 (t80)
REVERT: C  248 ASP cc_start: 0.7804 (t0) cc_final: 0.6752 (t0)
REVERT: C  251 GLU cc_start: 0.7485 (pm20) cc_final: 0.7051 (pm20)
REVERT: C  323 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8694 (tp)
REVERT: C  334 ARG cc_start: 0.6643 (tmt170) cc_final: 0.5615 (ttt180)
REVERT: D  149 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6915 (p90)
  outliers start: 46
  outliers final: 36
  residues processed: 259
  average time/residue: 0.1683
  time to fit residues: 60.9097
Evaluate side-chains
  269 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 228
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
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  260 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  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  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  224 TYR
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  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  364 LEU
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   64 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:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.121431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.099554 restraints weight = 18064.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.101338 restraints weight = 11072.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.102312 restraints weight = 8600.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.4710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7846  Z= 0.232
  Angle     :  0.741  10.507  10652  Z= 0.378
  Chirality :  0.045   0.341   1138
  Planarity :  0.005   0.050   1296
  Dihedral  :  7.255  56.764   1074
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 28.78 %
    Favored  : 66.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.28), residues: 886
  helix:  1.06 (0.21), residues: 564
  sheet: -0.46 (0.69), residues: 56
  loop : -3.33 (0.33), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C  84 
 HIS   0.003   0.001   HIS C 319 
 PHE   0.020   0.001   PHE A 310 
 TYR   0.030   0.002   TYR B  92 
 ARG   0.007   0.000   ARG A 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
  277 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 235
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.8724 (tpp) cc_final: 0.8249 (tpp)
REVERT: A  203 ASN cc_start: 0.8581 (t0) cc_final: 0.8319 (t0)
REVERT: A  224 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7195 (t80)
REVERT: A  233 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8000 (tm-30)
REVERT: A  334 ARG cc_start: 0.6888 (tmt170) cc_final: 0.5721 (ttm170)
REVERT: B   93 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7807 (tm-30)
REVERT: B  149 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7079 (p90)
REVERT: C   91 LEU cc_start: 0.8297 (pp) cc_final: 0.8070 (pp)
REVERT: C  140 MET cc_start: 0.8692 (tpp) cc_final: 0.8422 (tpp)
REVERT: C  248 ASP cc_start: 0.8012 (t0) cc_final: 0.6702 (t0)
REVERT: C  251 GLU cc_start: 0.7504 (pm20) cc_final: 0.6760 (pm20)
REVERT: C  334 ARG cc_start: 0.6852 (tmt170) cc_final: 0.5739 (ttt180)
REVERT: D   97 GLU cc_start: 0.8252 (tt0) cc_final: 0.8000 (tt0)
REVERT: D  118 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8058 (tm-30)
REVERT: D  149 HIS cc_start: 0.7578 (OUTLIER) cc_final: 0.6924 (p90)
  outliers start: 42
  outliers final: 35
  residues processed: 256
  average time/residue: 0.1628
  time to fit residues: 59.0485
Evaluate side-chains
  264 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 226
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
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  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  260 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  100 SER
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  236 CYS
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain C residue  260 LEU
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  263 ILE
Chi-restraints excluded: chain C residue  268 VAL
Chi-restraints excluded: chain C residue  372 LEU
Chi-restraints excluded: chain D residue   27 CYS
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  149 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0060
   chunk 49 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0870
   chunk 57 optimal weight:    5.9990
   chunk 87 optimal weight:    0.2980
   overall best weight:    0.4576

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.123895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.102293 restraints weight = 17806.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.104250 restraints weight = 10971.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.105182 restraints weight = 8428.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.4969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7846  Z= 0.211
  Angle     :  0.739  10.256  10652  Z= 0.376
  Chirality :  0.044   0.163   1138
  Planarity :  0.005   0.050   1296
  Dihedral  :  7.055  59.775   1070
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 30.02 %
    Favored  : 65.51 %
  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: -0.34 (0.28), residues: 886
  helix:  1.17 (0.21), residues: 560
  sheet: -0.43 (0.71), residues: 56
  loop : -3.31 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  84 
 HIS   0.004   0.001   HIS C 319 
 PHE   0.033   0.001   PHE B  24 
 TYR   0.034   0.002   TYR C 182 
 ARG   0.008   0.000   ARG A 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
  282 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 246
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 LEU cc_start: 0.8377 (pp) cc_final: 0.8115 (pp)
REVERT: A  140 MET cc_start: 0.8710 (tpp) cc_final: 0.8249 (tpp)
REVERT: A  177 MET cc_start: 0.7781 (tpp) cc_final: 0.7005 (tpp)
REVERT: A  203 ASN cc_start: 0.8569 (t0) cc_final: 0.8315 (t0)
REVERT: A  224 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7156 (t80)
REVERT: A  233 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8035 (tm-30)
REVERT: A  334 ARG cc_start: 0.6822 (tmt170) cc_final: 0.5650 (ttm170)
REVERT: B   44 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9110 (t)
REVERT: B  147 ILE cc_start: 0.9436 (tp) cc_final: 0.9213 (tp)
REVERT: B  149 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6915 (p90)
REVERT: C   91 LEU cc_start: 0.8374 (pp) cc_final: 0.8121 (pp)
REVERT: C  140 MET cc_start: 0.8669 (tpp) cc_final: 0.8382 (tpp)
REVERT: C  174 MET cc_start: 0.8919 (mmp) cc_final: 0.8629 (mmp)
REVERT: C  251 GLU cc_start: 0.7455 (pm20) cc_final: 0.6914 (pm20)
REVERT: D  149 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6872 (p90)
  outliers start: 36
  outliers final: 29
  residues processed: 263
  average time/residue: 0.1629
  time to fit residues: 59.9701
Evaluate side-chains
  265 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 232
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
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  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  100 SER
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  149 HIS
Chi-restraints excluded: chain C residue   82 HIS
Chi-restraints excluded: chain C residue  113 PHE
Chi-restraints excluded: chain C residue  210 THR
Chi-restraints excluded: chain C residue  219 LEU
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  282 MET
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   64 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:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0980
   chunk 54 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0670
   chunk 81 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
D  52 HIS
D 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.125112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.103617 restraints weight = 17651.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.105576 restraints weight = 10883.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.106495 restraints weight = 8360.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7846  Z= 0.219
  Angle     :  0.758  10.269  10652  Z= 0.389
  Chirality :  0.044   0.174   1138
  Planarity :  0.006   0.057   1296
  Dihedral  :  6.940  59.098   1070
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 30.15 %
    Favored  : 65.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.28), residues: 886
  helix:  1.18 (0.21), residues: 562
  sheet: -0.37 (0.73), residues: 56
  loop : -3.39 (0.32), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  84 
 HIS   0.005   0.001   HIS C 319 
 PHE   0.031   0.002   PHE B  24 
 TYR   0.027   0.002   TYR B  92 
 ARG   0.007   0.000   ARG A 156 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2411.81 seconds
wall clock time: 44 minutes 6.78 seconds (2646.78 seconds total)