Starting phenix.real_space_refine
on Tue Jan 14 01:13:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ja6_61291/01_2025/9ja6_61291.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ja6_61291/01_2025/9ja6_61291.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ja6_61291/01_2025/9ja6_61291.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ja6_61291/01_2025/9ja6_61291.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ja6_61291/01_2025/9ja6_61291.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ja6_61291/01_2025/9ja6_61291.cif"
  }
  resolution = 4.4
  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=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3020      2.51       5
     N     884      2.21       5
     O     948      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 4880
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1220
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 6, 'TRANS': 140}
    Chain: "B"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1220
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 6, 'TRANS': 140}
    Chain: "C"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1220
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 6, 'TRANS': 140}
    Chain: "D"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1220
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 6, 'TRANS': 140}
  Time building chain proxies: 3.74, per 1000 atoms: 0.77
  Number of scatterers: 4880
  At special positions: 0
  Unit cell: (92, 92, 120, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     948      8.00
     N     884      7.00
     C    3020      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 579.1 milliseconds
  

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1136

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      72.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 208 through 274
      removed outlier: 3.811A  pdb=" N   SER A 274 " --> pdb=" O   MET A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 305
      removed outlier: 3.672A  pdb=" N   ILE A 303 " --> pdb=" O   ARG A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 318
    Processing helix  chain 'A' and resid 326 through 328
      No H-bonds generated for 'chain 'A' and resid 326 through 328'
    Processing helix  chain 'A' and resid 329 through 339
    Processing helix  chain 'A' and resid 342 through 348
    Processing helix  chain 'B' and resid 209 through 274
      removed outlier: 3.810A  pdb=" N   SER B 274 " --> pdb=" O   MET B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 305
      removed outlier: 3.672A  pdb=" N   ILE B 303 " --> pdb=" O   ARG B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 318
    Processing helix  chain 'B' and resid 326 through 328
      No H-bonds generated for 'chain 'B' and resid 326 through 328'
    Processing helix  chain 'B' and resid 329 through 339
    Processing helix  chain 'B' and resid 342 through 348
    Processing helix  chain 'C' and resid 209 through 274
      removed outlier: 3.810A  pdb=" N   SER C 274 " --> pdb=" O   MET C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 305
      removed outlier: 3.672A  pdb=" N   ILE C 303 " --> pdb=" O   ARG C 299 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 318
    Processing helix  chain 'C' and resid 326 through 328
      No H-bonds generated for 'chain 'C' and resid 326 through 328'
    Processing helix  chain 'C' and resid 329 through 339
    Processing helix  chain 'C' and resid 342 through 348
    Processing helix  chain 'D' and resid 209 through 274
      removed outlier: 3.810A  pdb=" N   SER D 274 " --> pdb=" O   MET D 270 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 299 through 305
      removed outlier: 3.672A  pdb=" N   ILE D 303 " --> pdb=" O   ARG D 299 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 307 through 318
    Processing helix  chain 'D' and resid 326 through 328
      No H-bonds generated for 'chain 'D' and resid 326 through 328'
    Processing helix  chain 'D' and resid 329 through 339
    Processing helix  chain 'D' and resid 342 through 348

    325 hydrogen bonds defined for protein.
    975 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: 1.26

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1629
        1.33 -     1.45: 605
        1.45 -     1.57: 2678
        1.57 -     1.69: 0
        1.69 -     1.80: 52
  Bond restraints: 4964
  Sorted by residual:
  bond pdb=" CA  GLU A 217 "
       pdb=" C   GLU A 217 "
    ideal  model  delta    sigma   weight residual
    1.523  1.480  0.043 1.30e-02 5.92e+03 1.12e+01
  bond pdb=" CA  ALA C 214 "
       pdb=" C   ALA C 214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.480  0.043 1.30e-02 5.92e+03 1.08e+01
  bond pdb=" CA  ALA B 214 "
       pdb=" C   ALA B 214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.482  0.041 1.30e-02 5.92e+03 9.97e+00
  bond pdb=" CA  ALA A 214 "
       pdb=" C   ALA A 214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.482  0.041 1.30e-02 5.92e+03 9.95e+00
  bond pdb=" CA  ALA D 214 "
       pdb=" C   ALA D 214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.040 1.30e-02 5.92e+03 9.55e+00
  ... (remaining 4959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 6483
        2.29 -     4.58: 173
        4.58 -     6.87: 21
        6.87 -     9.17: 3
        9.17 -    11.46: 4
  Bond angle restraints: 6684
  Sorted by residual:
  angle pdb=" N   ALA C 214 "
        pdb=" CA  ALA C 214 "
        pdb=" C   ALA C 214 "
      ideal   model   delta    sigma   weight residual
     111.28  105.93    5.35 1.09e+00 8.42e-01 2.41e+01
  angle pdb=" N   GLU A 217 "
        pdb=" CA  GLU A 217 "
        pdb=" C   GLU A 217 "
      ideal   model   delta    sigma   weight residual
     111.28  106.10    5.18 1.09e+00 8.42e-01 2.26e+01
  angle pdb=" N   ALA B 214 "
        pdb=" CA  ALA B 214 "
        pdb=" C   ALA B 214 "
      ideal   model   delta    sigma   weight residual
     111.28  106.50    4.78 1.09e+00 8.42e-01 1.92e+01
  angle pdb=" N   ALA A 214 "
        pdb=" CA  ALA A 214 "
        pdb=" C   ALA A 214 "
      ideal   model   delta    sigma   weight residual
     111.28  106.54    4.74 1.09e+00 8.42e-01 1.89e+01
  angle pdb=" N   GLU D 217 "
        pdb=" CA  GLU D 217 "
        pdb=" C   GLU D 217 "
      ideal   model   delta    sigma   weight residual
     111.28  107.08    4.20 1.09e+00 8.42e-01 1.48e+01
  ... (remaining 6679 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 2662
       17.14 -    34.29: 313
       34.29 -    51.43: 88
       51.43 -    68.58: 29
       68.58 -    85.72: 4
  Dihedral angle restraints: 3096
    sinusoidal: 1356
      harmonic: 1740
  Sorted by residual:
  dihedral pdb=" CA  ARG C 299 "
           pdb=" C   ARG C 299 "
           pdb=" N   ILE C 300 "
           pdb=" CA  ILE C 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.64  -17.36     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  ARG B 299 "
           pdb=" C   ARG B 299 "
           pdb=" N   ILE B 300 "
           pdb=" CA  ILE B 300 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.65  -17.35     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ARG D 299 "
           pdb=" C   ARG D 299 "
           pdb=" N   ILE D 300 "
           pdb=" CA  ILE D 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.67  -17.33     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 3093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 330
       0.027 -    0.054: 214
       0.054 -    0.082: 128
       0.082 -    0.109: 22
       0.109 -    0.136: 10
  Chirality restraints: 704
  Sorted by residual:
  chirality pdb=" CG  LEU D 264 "
            pdb=" CB  LEU D 264 "
            pdb=" CD1 LEU D 264 "
            pdb=" CD2 LEU D 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CG  LEU C 264 "
            pdb=" CB  LEU C 264 "
            pdb=" CD1 LEU C 264 "
            pdb=" CD2 LEU C 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CG  LEU A 264 "
            pdb=" CB  LEU A 264 "
            pdb=" CD1 LEU A 264 "
            pdb=" CD2 LEU A 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 701 not shown)

  Planarity restraints: 888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 216 "   -0.010 2.00e-02 2.50e+03   2.08e-02 4.35e+00
        pdb=" C   GLU C 216 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLU C 216 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLU C 217 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 216 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.43e+00
        pdb=" C   GLU A 216 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   GLU A 216 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 217 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 213 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.73e+00
        pdb=" C   LYS B 213 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LYS B 213 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA B 214 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 885 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 975
        2.75 -     3.29: 5306
        3.29 -     3.82: 8175
        3.82 -     4.36: 9288
        4.36 -     4.90: 13784
  Nonbonded interactions: 37528
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 304 "
            pdb=" NZ  LYS D 331 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OD1 ASP B 304 "
            pdb=" NZ  LYS B 331 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OD1 ASP C 304 "
            pdb=" NZ  LYS C 331 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OD1 ASP A 304 "
            pdb=" NZ  LYS A 331 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OD2 ASP B 304 "
            pdb=" OH  TYR B 348 "
     model   vdw
     2.249 3.040
  ... (remaining 37523 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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:             2.280
  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:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.650
  Find NCS groups from input model:        0.190
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6396
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      :  0.008   0.047   4964  Z= 0.512
  Angle     :  0.942  11.457   6684  Z= 0.560
  Chirality :  0.043   0.136    704
  Planarity :  0.004   0.021    888
  Dihedral  : 16.510  85.724   1960
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 19.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  9.56 %
    Allowed  :  9.74 %
    Favored  : 80.70 %
  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: -1.98 (0.32), residues: 580
  helix: -1.17 (0.22), residues: 412
  sheet:  None (None), residues: 0
  loop : -1.24 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 221 
 PHE   0.010   0.002   PHE C 275 
 TYR   0.012   0.002   TYR C 344 
 ARG   0.004   0.001   ARG D 222 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 238
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 GLU cc_start: 0.7273 (mp0) cc_final: 0.6856 (mp0)
REVERT: A  270 MET cc_start: 0.8052 (mtp) cc_final: 0.7609 (mtp)
REVERT: A  282 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8355 (p)
REVERT: A  331 LYS cc_start: 0.8465 (mttt) cc_final: 0.8135 (mttt)
REVERT: B  220 GLU cc_start: 0.7569 (mp0) cc_final: 0.7185 (mp0)
REVERT: B  242 VAL cc_start: 0.8695 (t) cc_final: 0.8396 (t)
REVERT: B  260 MET cc_start: 0.5681 (ttp) cc_final: 0.5273 (ttp)
REVERT: B  314 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.8027 (m-10)
REVERT: B  325 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6694 (p0)
REVERT: B  331 LYS cc_start: 0.8148 (mttt) cc_final: 0.7828 (mtpt)
REVERT: C  222 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8282 (mtt-85)
REVERT: C  242 VAL cc_start: 0.8918 (t) cc_final: 0.8717 (t)
REVERT: C  260 MET cc_start: 0.5597 (ttp) cc_final: 0.5340 (ttp)
REVERT: C  270 MET cc_start: 0.8300 (mtp) cc_final: 0.7692 (ttm)
REVERT: C  286 ASN cc_start: 0.7916 (p0) cc_final: 0.7650 (p0)
REVERT: C  304 ASP cc_start: 0.5186 (t0) cc_final: 0.4412 (t0)
REVERT: C  308 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7271 (tm-30)
REVERT: C  316 LYS cc_start: 0.8920 (tppp) cc_final: 0.8709 (tppp)
REVERT: C  325 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.6007 (p0)
REVERT: C  331 LYS cc_start: 0.8079 (mttt) cc_final: 0.7783 (mttt)
REVERT: D  260 MET cc_start: 0.5585 (ttp) cc_final: 0.4938 (ttp)
REVERT: D  270 MET cc_start: 0.8373 (mtp) cc_final: 0.7419 (mmm)
REVERT: D  286 ASN cc_start: 0.7794 (p0) cc_final: 0.7526 (p0)
REVERT: D  304 ASP cc_start: 0.5297 (t0) cc_final: 0.4719 (t0)
REVERT: D  314 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8047 (m-10)
  outliers start: 52
  outliers final: 18
  residues processed: 271
  average time/residue: 0.2275
  time to fit residues: 73.0878
Evaluate side-chains
  250 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 226
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN
C 231 ASN
D 231 ASN
D 267 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.104834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.087607 restraints weight = 12630.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.091284 restraints weight = 7033.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.093913 restraints weight = 4536.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4964  Z= 0.180
  Angle     :  0.562   6.190   6684  Z= 0.307
  Chirality :  0.040   0.146    704
  Planarity :  0.005   0.045    888
  Dihedral  :  4.104  18.022    668
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.86 %
    Favored  : 95.96 %
  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:  1.63 (0.35), residues: 580
  helix:  1.61 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop : -0.15 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 330 
 PHE   0.008   0.001   PHE C 284 
 TYR   0.008   0.001   TYR B 314 
 ARG   0.005   0.001   ARG B 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.7933 (mmm) cc_final: 0.7722 (mmm)
REVERT: A  213 LYS cc_start: 0.9068 (mttt) cc_final: 0.8748 (mttt)
REVERT: A  220 GLU cc_start: 0.7971 (mp0) cc_final: 0.7471 (mp0)
REVERT: A  222 ARG cc_start: 0.8630 (mtt-85) cc_final: 0.7738 (mtp85)
REVERT: A  247 ARG cc_start: 0.8940 (ttm170) cc_final: 0.8679 (ttm170)
REVERT: A  262 MET cc_start: 0.7755 (tmm) cc_final: 0.7289 (tmm)
REVERT: A  272 MET cc_start: 0.8401 (mmt) cc_final: 0.7980 (mmt)
REVERT: A  275 PHE cc_start: 0.8635 (m-80) cc_final: 0.8244 (m-80)
REVERT: A  282 VAL cc_start: 0.8968 (t) cc_final: 0.8712 (p)
REVERT: A  299 ARG cc_start: 0.7962 (ttm170) cc_final: 0.7632 (ttm170)
REVERT: A  309 GLU cc_start: 0.8723 (pm20) cc_final: 0.8422 (pp20)
REVERT: A  316 LYS cc_start: 0.8908 (tppp) cc_final: 0.8470 (mttt)
REVERT: A  344 TYR cc_start: 0.7829 (t80) cc_final: 0.7627 (t80)
REVERT: B  208 MET cc_start: 0.7967 (mmm) cc_final: 0.7506 (mmm)
REVERT: B  217 GLU cc_start: 0.7525 (pp20) cc_final: 0.7295 (pp20)
REVERT: B  218 ASP cc_start: 0.7687 (m-30) cc_final: 0.6510 (m-30)
REVERT: B  222 ARG cc_start: 0.8752 (mtt-85) cc_final: 0.8500 (mtt-85)
REVERT: B  227 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8288 (mm-30)
REVERT: B  246 MET cc_start: 0.8928 (mtp) cc_final: 0.8429 (mtp)
REVERT: B  249 ASP cc_start: 0.8584 (t70) cc_final: 0.8112 (t0)
REVERT: B  270 MET cc_start: 0.8076 (mtp) cc_final: 0.7587 (mtp)
REVERT: B  275 PHE cc_start: 0.8756 (m-80) cc_final: 0.8155 (m-80)
REVERT: B  299 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7825 (ttm170)
REVERT: B  304 ASP cc_start: 0.7169 (t0) cc_final: 0.6881 (t0)
REVERT: B  316 LYS cc_start: 0.8894 (mmtp) cc_final: 0.8384 (mmtp)
REVERT: B  322 TYR cc_start: 0.6055 (p90) cc_final: 0.5715 (p90)
REVERT: B  344 TYR cc_start: 0.8454 (t80) cc_final: 0.8232 (t80)
REVERT: C  211 TRP cc_start: 0.8246 (m100) cc_final: 0.7850 (m100)
REVERT: C  212 LYS cc_start: 0.9256 (mttt) cc_final: 0.8914 (mmmt)
REVERT: C  217 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7949 (mt-10)
REVERT: C  222 ARG cc_start: 0.8980 (mtt-85) cc_final: 0.8427 (mtt-85)
REVERT: C  226 ASP cc_start: 0.8513 (t0) cc_final: 0.8262 (t0)
REVERT: C  227 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8467 (mm-30)
REVERT: C  246 MET cc_start: 0.8763 (mtp) cc_final: 0.8297 (mtp)
REVERT: C  248 ASN cc_start: 0.9055 (m-40) cc_final: 0.8819 (m-40)
REVERT: C  249 ASP cc_start: 0.8553 (t70) cc_final: 0.8186 (t70)
REVERT: C  260 MET cc_start: 0.7645 (ttp) cc_final: 0.7436 (ttp)
REVERT: C  262 MET cc_start: 0.8036 (tmm) cc_final: 0.7231 (tmm)
REVERT: C  275 PHE cc_start: 0.8739 (m-80) cc_final: 0.8200 (m-80)
REVERT: C  282 VAL cc_start: 0.8905 (t) cc_final: 0.8011 (p)
REVERT: C  296 ARG cc_start: 0.7776 (ttt90) cc_final: 0.7447 (ttt90)
REVERT: C  304 ASP cc_start: 0.6790 (t0) cc_final: 0.5900 (t0)
REVERT: C  316 LYS cc_start: 0.8931 (tppp) cc_final: 0.8573 (tppp)
REVERT: C  344 TYR cc_start: 0.8591 (t80) cc_final: 0.8203 (t80)
REVERT: C  348 TYR cc_start: 0.8110 (t80) cc_final: 0.7687 (t80)
REVERT: D  212 LYS cc_start: 0.8927 (mmtm) cc_final: 0.8636 (mmmt)
REVERT: D  242 VAL cc_start: 0.8969 (t) cc_final: 0.8756 (t)
REVERT: D  245 ASP cc_start: 0.8872 (m-30) cc_final: 0.8565 (m-30)
REVERT: D  262 MET cc_start: 0.8023 (tmm) cc_final: 0.7639 (tmm)
REVERT: D  282 VAL cc_start: 0.8902 (t) cc_final: 0.8697 (p)
REVERT: D  331 LYS cc_start: 0.8640 (mttt) cc_final: 0.8369 (mttt)
REVERT: D  344 TYR cc_start: 0.8583 (t80) cc_final: 0.8335 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 225
  average time/residue: 0.2199
  time to fit residues: 59.1839
Evaluate side-chains
  213 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 243 GLN
B 243 GLN
C 243 GLN
C 252 ASN
C 310 ASN
C 327 GLN
D 243 GLN
D 327 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.098574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.083279 restraints weight = 12836.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.086902 restraints weight = 6684.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.089476 restraints weight = 4149.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.5500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4964  Z= 0.195
  Angle     :  0.538   6.196   6684  Z= 0.312
  Chirality :  0.039   0.149    704
  Planarity :  0.004   0.039    888
  Dihedral  :  3.924  17.503    668
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.35), residues: 580
  helix:  2.21 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.11 (0.55), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP D 211 
 PHE   0.007   0.001   PHE A 284 
 TYR   0.007   0.001   TYR C 314 
 ARG   0.003   0.000   ARG B 259 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.8034 (mmm) cc_final: 0.7762 (mmm)
REVERT: A  213 LYS cc_start: 0.9005 (mttt) cc_final: 0.8650 (mttt)
REVERT: A  222 ARG cc_start: 0.8631 (mtt-85) cc_final: 0.7721 (mtp85)
REVERT: A  227 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8232 (mm-30)
REVERT: A  262 MET cc_start: 0.7926 (tmm) cc_final: 0.7305 (tmm)
REVERT: A  270 MET cc_start: 0.8177 (mtp) cc_final: 0.7872 (mtp)
REVERT: A  272 MET cc_start: 0.8255 (mmt) cc_final: 0.8047 (mmp)
REVERT: A  275 PHE cc_start: 0.8748 (m-80) cc_final: 0.8236 (m-80)
REVERT: A  282 VAL cc_start: 0.8832 (t) cc_final: 0.8505 (p)
REVERT: A  299 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7571 (ttm170)
REVERT: A  309 GLU cc_start: 0.8818 (pm20) cc_final: 0.8573 (pp20)
REVERT: A  316 LYS cc_start: 0.8971 (tppp) cc_final: 0.8598 (tppp)
REVERT: A  344 TYR cc_start: 0.7950 (t80) cc_final: 0.7700 (t80)
REVERT: B  208 MET cc_start: 0.8077 (mmm) cc_final: 0.7466 (mmm)
REVERT: B  211 TRP cc_start: 0.8237 (m100) cc_final: 0.7414 (m100)
REVERT: B  222 ARG cc_start: 0.8812 (mtt-85) cc_final: 0.8222 (mtt-85)
REVERT: B  246 MET cc_start: 0.8937 (mtp) cc_final: 0.8589 (mtp)
REVERT: B  275 PHE cc_start: 0.8687 (m-80) cc_final: 0.8105 (m-80)
REVERT: B  282 VAL cc_start: 0.8827 (t) cc_final: 0.8448 (p)
REVERT: B  299 ARG cc_start: 0.8018 (ttm170) cc_final: 0.7681 (ttm170)
REVERT: B  314 TYR cc_start: 0.8457 (m-10) cc_final: 0.8223 (m-10)
REVERT: B  316 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8262 (mmtp)
REVERT: B  331 LYS cc_start: 0.9106 (mtpt) cc_final: 0.8067 (ttmt)
REVERT: B  344 TYR cc_start: 0.8430 (t80) cc_final: 0.8163 (t80)
REVERT: C  212 LYS cc_start: 0.9319 (mttt) cc_final: 0.9000 (mmmt)
REVERT: C  217 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7933 (mt-10)
REVERT: C  222 ARG cc_start: 0.8962 (mtt-85) cc_final: 0.8487 (mtt-85)
REVERT: C  226 ASP cc_start: 0.8593 (t0) cc_final: 0.8271 (t0)
REVERT: C  227 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8483 (mm-30)
REVERT: C  246 MET cc_start: 0.9019 (mtp) cc_final: 0.8588 (mtp)
REVERT: C  249 ASP cc_start: 0.8593 (t70) cc_final: 0.8222 (t70)
REVERT: C  250 LEU cc_start: 0.8643 (tp) cc_final: 0.8192 (tp)
REVERT: C  262 MET cc_start: 0.8001 (tmm) cc_final: 0.7210 (tmm)
REVERT: C  270 MET cc_start: 0.8602 (ttm) cc_final: 0.7796 (tpt)
REVERT: C  275 PHE cc_start: 0.8768 (m-80) cc_final: 0.8187 (m-80)
REVERT: C  282 VAL cc_start: 0.8794 (t) cc_final: 0.7832 (p)
REVERT: C  296 ARG cc_start: 0.7753 (ttt90) cc_final: 0.7281 (ttt90)
REVERT: C  304 ASP cc_start: 0.6899 (t0) cc_final: 0.6041 (t0)
REVERT: C  316 LYS cc_start: 0.8807 (tppp) cc_final: 0.8401 (tppp)
REVERT: C  331 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8246 (tttt)
REVERT: C  344 TYR cc_start: 0.8507 (t80) cc_final: 0.8102 (t80)
REVERT: D  212 LYS cc_start: 0.9005 (mmtm) cc_final: 0.8681 (mmmt)
REVERT: D  218 ASP cc_start: 0.7722 (m-30) cc_final: 0.7257 (m-30)
REVERT: D  242 VAL cc_start: 0.9000 (t) cc_final: 0.8745 (t)
REVERT: D  244 ARG cc_start: 0.8792 (ttm170) cc_final: 0.8451 (ttm170)
REVERT: D  245 ASP cc_start: 0.8888 (m-30) cc_final: 0.8558 (m-30)
REVERT: D  249 ASP cc_start: 0.8628 (t70) cc_final: 0.7972 (t70)
REVERT: D  262 MET cc_start: 0.7971 (tmm) cc_final: 0.7551 (tmm)
REVERT: D  266 ARG cc_start: 0.8315 (ttp-170) cc_final: 0.8060 (ttp80)
REVERT: D  268 ASN cc_start: 0.8412 (m-40) cc_final: 0.8171 (m-40)
REVERT: D  270 MET cc_start: 0.8490 (ttm) cc_final: 0.7869 (tpt)
REVERT: D  275 PHE cc_start: 0.8788 (m-10) cc_final: 0.8366 (m-10)
REVERT: D  282 VAL cc_start: 0.8793 (t) cc_final: 0.8476 (p)
REVERT: D  304 ASP cc_start: 0.7186 (t0) cc_final: 0.6873 (t0)
REVERT: D  309 GLU cc_start: 0.8906 (pm20) cc_final: 0.8527 (pp20)
REVERT: D  313 ARG cc_start: 0.8911 (mmp80) cc_final: 0.8531 (mmp80)
REVERT: D  316 LYS cc_start: 0.8694 (mmmm) cc_final: 0.7885 (mmmm)
REVERT: D  327 GLN cc_start: 0.6955 (mp10) cc_final: 0.6708 (mp10)
REVERT: D  331 LYS cc_start: 0.8767 (mttt) cc_final: 0.8071 (ttmt)
REVERT: D  344 TYR cc_start: 0.8521 (t80) cc_final: 0.8279 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.2610
  time to fit residues: 66.8096
Evaluate side-chains
  215 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 0 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 7 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
B 231 ASN
B 269 ASN
B 310 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.096231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.081631 restraints weight = 12975.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.085167 restraints weight = 6605.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.087571 restraints weight = 4017.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.6440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4964  Z= 0.202
  Angle     :  0.532   5.137   6684  Z= 0.310
  Chirality :  0.040   0.161    704
  Planarity :  0.004   0.031    888
  Dihedral  :  3.955  20.662    668
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.36), residues: 580
  helix:  2.34 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.33 (0.58), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP D 211 
 PHE   0.006   0.001   PHE B 350 
 TYR   0.016   0.001   TYR C 314 
 ARG   0.005   0.000   ARG C 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.8233 (mmm) cc_final: 0.8012 (mmm)
REVERT: A  213 LYS cc_start: 0.8971 (mttt) cc_final: 0.8623 (mttt)
REVERT: A  222 ARG cc_start: 0.8821 (mtt-85) cc_final: 0.8431 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8365 (mm-30)
REVERT: A  242 VAL cc_start: 0.9244 (p) cc_final: 0.8949 (p)
REVERT: A  262 MET cc_start: 0.8040 (tmm) cc_final: 0.7544 (tmm)
REVERT: A  270 MET cc_start: 0.8211 (mtp) cc_final: 0.7671 (mtp)
REVERT: A  272 MET cc_start: 0.7908 (mmm) cc_final: 0.7465 (mmm)
REVERT: A  275 PHE cc_start: 0.8772 (m-80) cc_final: 0.8256 (m-80)
REVERT: A  299 ARG cc_start: 0.7924 (ttm170) cc_final: 0.7667 (ttm170)
REVERT: A  309 GLU cc_start: 0.8942 (pm20) cc_final: 0.8650 (pp20)
REVERT: A  316 LYS cc_start: 0.8945 (tppp) cc_final: 0.8551 (tppp)
REVERT: A  344 TYR cc_start: 0.8045 (t80) cc_final: 0.7820 (t80)
REVERT: A  348 TYR cc_start: 0.7822 (t80) cc_final: 0.7564 (t80)
REVERT: B  213 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8536 (mtmm)
REVERT: B  222 ARG cc_start: 0.8805 (mtt-85) cc_final: 0.8303 (mtt-85)
REVERT: B  268 ASN cc_start: 0.8356 (m-40) cc_final: 0.8151 (m-40)
REVERT: B  272 MET cc_start: 0.7714 (mmp) cc_final: 0.7361 (mmp)
REVERT: B  275 PHE cc_start: 0.8731 (m-80) cc_final: 0.8146 (m-80)
REVERT: B  282 VAL cc_start: 0.8778 (t) cc_final: 0.8487 (p)
REVERT: B  299 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7687 (ttm170)
REVERT: B  316 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8101 (mmtp)
REVERT: B  322 TYR cc_start: 0.6784 (p90) cc_final: 0.6159 (p90)
REVERT: B  331 LYS cc_start: 0.9108 (mttt) cc_final: 0.8047 (ttmm)
REVERT: B  344 TYR cc_start: 0.8461 (t80) cc_final: 0.8209 (t80)
REVERT: C  212 LYS cc_start: 0.9318 (mttt) cc_final: 0.9043 (mmmt)
REVERT: C  217 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7969 (mt-10)
REVERT: C  218 ASP cc_start: 0.8286 (m-30) cc_final: 0.7268 (m-30)
REVERT: C  222 ARG cc_start: 0.8971 (mtt-85) cc_final: 0.8519 (mtt-85)
REVERT: C  242 VAL cc_start: 0.9039 (t) cc_final: 0.8818 (t)
REVERT: C  244 ARG cc_start: 0.8710 (ttm110) cc_final: 0.8221 (ttm110)
REVERT: C  246 MET cc_start: 0.8960 (mtp) cc_final: 0.8495 (mtp)
REVERT: C  249 ASP cc_start: 0.8580 (t70) cc_final: 0.8224 (t70)
REVERT: C  262 MET cc_start: 0.8079 (tmm) cc_final: 0.7284 (tmm)
REVERT: C  270 MET cc_start: 0.8517 (ttm) cc_final: 0.8045 (tpp)
REVERT: C  275 PHE cc_start: 0.8810 (m-80) cc_final: 0.8250 (m-80)
REVERT: C  296 ARG cc_start: 0.7744 (ttt90) cc_final: 0.7351 (ttt90)
REVERT: C  316 LYS cc_start: 0.8796 (tppp) cc_final: 0.8349 (tppp)
REVERT: C  344 TYR cc_start: 0.8520 (t80) cc_final: 0.8131 (t80)
REVERT: D  212 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8817 (mmmt)
REVERT: D  218 ASP cc_start: 0.7783 (m-30) cc_final: 0.7417 (m-30)
REVERT: D  231 ASN cc_start: 0.9024 (m110) cc_final: 0.8820 (m-40)
REVERT: D  242 VAL cc_start: 0.8993 (t) cc_final: 0.8738 (t)
REVERT: D  244 ARG cc_start: 0.8799 (ttm170) cc_final: 0.8537 (ttm170)
REVERT: D  245 ASP cc_start: 0.8934 (m-30) cc_final: 0.8615 (m-30)
REVERT: D  246 MET cc_start: 0.8627 (ptp) cc_final: 0.8422 (ptp)
REVERT: D  249 ASP cc_start: 0.8632 (t70) cc_final: 0.8121 (t70)
REVERT: D  262 MET cc_start: 0.7974 (tmm) cc_final: 0.7426 (tmm)
REVERT: D  270 MET cc_start: 0.8552 (ttm) cc_final: 0.7844 (mmm)
REVERT: D  275 PHE cc_start: 0.8774 (m-10) cc_final: 0.8373 (m-10)
REVERT: D  282 VAL cc_start: 0.8825 (t) cc_final: 0.8534 (p)
REVERT: D  309 GLU cc_start: 0.8962 (pm20) cc_final: 0.8446 (pp20)
REVERT: D  313 ARG cc_start: 0.8911 (mmp80) cc_final: 0.8515 (mmp80)
REVERT: D  316 LYS cc_start: 0.8650 (mmmm) cc_final: 0.7842 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2647
  time to fit residues: 64.6448
Evaluate side-chains
  207 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    0.2980
   chunk 6 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 252 ASN
B 231 ASN
** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.095011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.080893 restraints weight = 13039.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.084341 restraints weight = 6513.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.086542 restraints weight = 3927.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.7225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4964  Z= 0.235
  Angle     :  0.569   7.020   6684  Z= 0.330
  Chirality :  0.040   0.143    704
  Planarity :  0.004   0.029    888
  Dihedral  :  4.167  21.124    668
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.12 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.35), residues: 580
  helix:  2.22 (0.23), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.20 (0.57), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 330 
 PHE   0.009   0.001   PHE B 350 
 TYR   0.019   0.002   TYR C 314 
 ARG   0.006   0.000   ARG B 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 218
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.8165 (mmm) cc_final: 0.7646 (mmm)
REVERT: A  211 TRP cc_start: 0.8144 (m100) cc_final: 0.6950 (m100)
REVERT: A  217 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7643 (pm20)
REVERT: A  222 ARG cc_start: 0.8844 (mtt-85) cc_final: 0.8582 (mtt-85)
REVERT: A  242 VAL cc_start: 0.9325 (p) cc_final: 0.8941 (p)
REVERT: A  262 MET cc_start: 0.8090 (tmm) cc_final: 0.7502 (tmm)
REVERT: A  267 ASN cc_start: 0.8063 (t0) cc_final: 0.7617 (t0)
REVERT: A  270 MET cc_start: 0.8338 (mtp) cc_final: 0.7818 (mtp)
REVERT: A  272 MET cc_start: 0.7809 (mmm) cc_final: 0.7335 (mmm)
REVERT: A  275 PHE cc_start: 0.8707 (m-80) cc_final: 0.8209 (m-80)
REVERT: A  299 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7722 (ttm170)
REVERT: A  309 GLU cc_start: 0.9010 (pm20) cc_final: 0.8514 (pp20)
REVERT: A  310 ASN cc_start: 0.8952 (m-40) cc_final: 0.7792 (m-40)
REVERT: A  313 ARG cc_start: 0.8949 (mtp180) cc_final: 0.8591 (mtp180)
REVERT: A  316 LYS cc_start: 0.8934 (tppp) cc_final: 0.8475 (tppp)
REVERT: A  332 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8479 (tpt170)
REVERT: A  348 TYR cc_start: 0.7841 (t80) cc_final: 0.7564 (t80)
REVERT: B  217 GLU cc_start: 0.7567 (pp20) cc_final: 0.7104 (pp20)
REVERT: B  218 ASP cc_start: 0.7921 (m-30) cc_final: 0.6774 (m-30)
REVERT: B  222 ARG cc_start: 0.8835 (mtt-85) cc_final: 0.8383 (mtt-85)
REVERT: B  275 PHE cc_start: 0.8680 (m-80) cc_final: 0.8122 (m-80)
REVERT: B  299 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7647 (ttm170)
REVERT: B  316 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8068 (mmtp)
REVERT: B  322 TYR cc_start: 0.6893 (p90) cc_final: 0.6546 (p90)
REVERT: B  331 LYS cc_start: 0.9107 (mttt) cc_final: 0.8096 (ttmm)
REVERT: B  344 TYR cc_start: 0.8463 (t80) cc_final: 0.8182 (t80)
REVERT: B  352 PRO cc_start: 0.8764 (Cg_exo) cc_final: 0.8536 (Cg_endo)
REVERT: C  212 LYS cc_start: 0.9351 (mttt) cc_final: 0.9116 (mmmt)
REVERT: C  217 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8039 (mt-10)
REVERT: C  218 ASP cc_start: 0.8409 (m-30) cc_final: 0.8020 (m-30)
REVERT: C  226 ASP cc_start: 0.8817 (t0) cc_final: 0.8528 (t0)
REVERT: C  229 LEU cc_start: 0.9256 (mt) cc_final: 0.9051 (mt)
REVERT: C  242 VAL cc_start: 0.9045 (t) cc_final: 0.8828 (t)
REVERT: C  244 ARG cc_start: 0.8683 (ttm110) cc_final: 0.8203 (ttm110)
REVERT: C  246 MET cc_start: 0.8887 (mtp) cc_final: 0.8492 (mtp)
REVERT: C  249 ASP cc_start: 0.8571 (t70) cc_final: 0.8164 (t70)
REVERT: C  250 LEU cc_start: 0.8741 (tp) cc_final: 0.8510 (tp)
REVERT: C  262 MET cc_start: 0.8065 (tmm) cc_final: 0.7251 (tmm)
REVERT: C  275 PHE cc_start: 0.8769 (m-80) cc_final: 0.8189 (m-80)
REVERT: C  282 VAL cc_start: 0.8750 (t) cc_final: 0.7759 (t)
REVERT: C  294 LEU cc_start: 0.8774 (mm) cc_final: 0.8552 (mm)
REVERT: C  299 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8160 (ttp-110)
REVERT: C  316 LYS cc_start: 0.8729 (tppp) cc_final: 0.8231 (tppp)
REVERT: C  344 TYR cc_start: 0.8551 (t80) cc_final: 0.8178 (t80)
REVERT: C  348 TYR cc_start: 0.8255 (t80) cc_final: 0.7966 (t80)
REVERT: D  212 LYS cc_start: 0.9138 (mmtm) cc_final: 0.8847 (mmmt)
REVERT: D  231 ASN cc_start: 0.9085 (m110) cc_final: 0.8875 (m-40)
REVERT: D  242 VAL cc_start: 0.9062 (t) cc_final: 0.8799 (t)
REVERT: D  244 ARG cc_start: 0.8775 (ttm170) cc_final: 0.8559 (ttm170)
REVERT: D  245 ASP cc_start: 0.8891 (m-30) cc_final: 0.8591 (m-30)
REVERT: D  262 MET cc_start: 0.7968 (tmm) cc_final: 0.7631 (tmm)
REVERT: D  270 MET cc_start: 0.8390 (ttm) cc_final: 0.8090 (ttm)
REVERT: D  276 ARG cc_start: 0.8589 (mtt180) cc_final: 0.8061 (mtt180)
REVERT: D  281 GLU cc_start: 0.8089 (tt0) cc_final: 0.7665 (tm-30)
REVERT: D  309 GLU cc_start: 0.9010 (pm20) cc_final: 0.8525 (pp20)
REVERT: D  313 ARG cc_start: 0.8892 (mmp80) cc_final: 0.8466 (mmp80)
REVERT: D  316 LYS cc_start: 0.8629 (mmmm) cc_final: 0.7821 (mmmm)
REVERT: D  322 TYR cc_start: 0.6916 (p90) cc_final: 0.6663 (p90)
REVERT: D  332 ARG cc_start: 0.8655 (mmt-90) cc_final: 0.8398 (mmt-90)
REVERT: D  348 TYR cc_start: 0.8175 (t80) cc_final: 0.7959 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2902
  time to fit residues: 72.4776
Evaluate side-chains
  218 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 28 optimal weight:    0.3980
   chunk 44 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 252 ASN
B 231 ASN
B 252 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN
** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.095813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.081361 restraints weight = 12878.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.084865 restraints weight = 6602.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.087244 restraints weight = 4043.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.7482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4964  Z= 0.150
  Angle     :  0.511   5.631   6684  Z= 0.293
  Chirality :  0.039   0.130    704
  Planarity :  0.004   0.028    888
  Dihedral  :  3.819  17.569    668
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  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:  3.09 (0.35), residues: 580
  helix:  2.74 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.29 (0.56), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 330 
 PHE   0.007   0.001   PHE C 284 
 TYR   0.015   0.001   TYR B 314 
 ARG   0.006   0.000   ARG A 255 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.8162 (mmm) cc_final: 0.7667 (mmm)
REVERT: A  211 TRP cc_start: 0.8157 (m100) cc_final: 0.6922 (m100)
REVERT: A  222 ARG cc_start: 0.8705 (mtt-85) cc_final: 0.8460 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: A  242 VAL cc_start: 0.9319 (p) cc_final: 0.8901 (p)
REVERT: A  262 MET cc_start: 0.8002 (tmm) cc_final: 0.7128 (tmm)
REVERT: A  270 MET cc_start: 0.8314 (mtp) cc_final: 0.7958 (mtp)
REVERT: A  272 MET cc_start: 0.7808 (mmm) cc_final: 0.7327 (mmm)
REVERT: A  275 PHE cc_start: 0.8711 (m-80) cc_final: 0.8223 (m-80)
REVERT: A  282 VAL cc_start: 0.8783 (t) cc_final: 0.8175 (t)
REVERT: A  299 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7713 (ttm170)
REVERT: A  309 GLU cc_start: 0.9031 (pm20) cc_final: 0.8535 (pp20)
REVERT: A  310 ASN cc_start: 0.8867 (m-40) cc_final: 0.7676 (m-40)
REVERT: A  313 ARG cc_start: 0.8933 (mtp180) cc_final: 0.8552 (mtp180)
REVERT: A  316 LYS cc_start: 0.8856 (tppp) cc_final: 0.8400 (tppp)
REVERT: A  332 ARG cc_start: 0.8880 (tpp80) cc_final: 0.8431 (tpt170)
REVERT: A  344 TYR cc_start: 0.8172 (t80) cc_final: 0.7793 (t80)
REVERT: A  348 TYR cc_start: 0.7859 (t80) cc_final: 0.7539 (t80)
REVERT: B  217 GLU cc_start: 0.7590 (pp20) cc_final: 0.7064 (pp20)
REVERT: B  218 ASP cc_start: 0.7918 (m-30) cc_final: 0.6680 (m-30)
REVERT: B  222 ARG cc_start: 0.8797 (mtt-85) cc_final: 0.8291 (mtt-85)
REVERT: B  246 MET cc_start: 0.8838 (mtp) cc_final: 0.8543 (mtp)
REVERT: B  249 ASP cc_start: 0.8538 (t70) cc_final: 0.8093 (t0)
REVERT: B  275 PHE cc_start: 0.8669 (m-80) cc_final: 0.8144 (m-80)
REVERT: B  282 VAL cc_start: 0.8724 (t) cc_final: 0.8441 (p)
REVERT: B  299 ARG cc_start: 0.7908 (ttm170) cc_final: 0.7632 (ttm170)
REVERT: B  316 LYS cc_start: 0.8699 (mmtp) cc_final: 0.7915 (mmtp)
REVERT: B  331 LYS cc_start: 0.9158 (mttt) cc_final: 0.8154 (ttmm)
REVERT: B  344 TYR cc_start: 0.8439 (t80) cc_final: 0.8128 (t80)
REVERT: B  352 PRO cc_start: 0.8694 (Cg_exo) cc_final: 0.8469 (Cg_endo)
REVERT: C  212 LYS cc_start: 0.9328 (mttt) cc_final: 0.9086 (mmmt)
REVERT: C  217 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7948 (mt-10)
REVERT: C  218 ASP cc_start: 0.8348 (m-30) cc_final: 0.7301 (m-30)
REVERT: C  222 ARG cc_start: 0.9013 (mtt-85) cc_final: 0.8478 (mtt-85)
REVERT: C  226 ASP cc_start: 0.8835 (t0) cc_final: 0.8459 (t0)
REVERT: C  242 VAL cc_start: 0.9059 (t) cc_final: 0.8796 (t)
REVERT: C  244 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8188 (ttm110)
REVERT: C  246 MET cc_start: 0.8844 (mtp) cc_final: 0.8462 (mtp)
REVERT: C  249 ASP cc_start: 0.8537 (t70) cc_final: 0.8188 (t70)
REVERT: C  250 LEU cc_start: 0.8669 (tp) cc_final: 0.8423 (tp)
REVERT: C  262 MET cc_start: 0.8008 (tmm) cc_final: 0.7161 (tmm)
REVERT: C  270 MET cc_start: 0.8553 (ttm) cc_final: 0.8307 (ttm)
REVERT: C  275 PHE cc_start: 0.8762 (m-80) cc_final: 0.8161 (m-80)
REVERT: C  282 VAL cc_start: 0.8748 (t) cc_final: 0.7807 (t)
REVERT: C  296 ARG cc_start: 0.7696 (ttt90) cc_final: 0.7364 (ttt90)
REVERT: C  316 LYS cc_start: 0.8670 (tppp) cc_final: 0.8132 (tppp)
REVERT: C  322 TYR cc_start: 0.7195 (p90) cc_final: 0.6864 (p90)
REVERT: C  331 LYS cc_start: 0.9108 (mtpt) cc_final: 0.8113 (ttmt)
REVERT: C  344 TYR cc_start: 0.8509 (t80) cc_final: 0.8099 (t80)
REVERT: D  212 LYS cc_start: 0.9133 (mmtm) cc_final: 0.8667 (mmmt)
REVERT: D  231 ASN cc_start: 0.9026 (m110) cc_final: 0.8816 (m-40)
REVERT: D  242 VAL cc_start: 0.9058 (t) cc_final: 0.8759 (t)
REVERT: D  244 ARG cc_start: 0.8761 (ttm170) cc_final: 0.8528 (ttm170)
REVERT: D  245 ASP cc_start: 0.8925 (m-30) cc_final: 0.8649 (m-30)
REVERT: D  262 MET cc_start: 0.7967 (tmm) cc_final: 0.7594 (tmm)
REVERT: D  276 ARG cc_start: 0.8590 (mtt180) cc_final: 0.8071 (mtt180)
REVERT: D  281 GLU cc_start: 0.8174 (tt0) cc_final: 0.7642 (tm-30)
REVERT: D  309 GLU cc_start: 0.8999 (pm20) cc_final: 0.8735 (pp20)
REVERT: D  313 ARG cc_start: 0.8869 (mmp80) cc_final: 0.8292 (mmp80)
REVERT: D  316 LYS cc_start: 0.8559 (mmmm) cc_final: 0.7777 (mmmm)
REVERT: D  322 TYR cc_start: 0.6773 (p90) cc_final: 0.6520 (p90)
REVERT: D  344 TYR cc_start: 0.8575 (t80) cc_final: 0.8102 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.3016
  time to fit residues: 72.1619
Evaluate side-chains
  207 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 25 optimal weight:    0.0030
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 42 optimal weight:    0.4980
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
A 267 ASN
A 269 ASN
B 231 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN
** C 268 ASN ** 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 = 0.3648 r_free = 0.3648 target = 0.096982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.082027 restraints weight = 12630.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.085551 restraints weight = 6467.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.087955 restraints weight = 3976.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.7616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4964  Z= 0.135
  Angle     :  0.500   6.774   6684  Z= 0.286
  Chirality :  0.038   0.131    704
  Planarity :  0.003   0.025    888
  Dihedral  :  3.668  18.442    668
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  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:  3.24 (0.36), residues: 580
  helix:  2.88 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.25 (0.56), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 330 
 PHE   0.005   0.001   PHE C 350 
 TYR   0.013   0.001   TYR A 314 
 ARG   0.006   0.000   ARG C 255 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 TRP cc_start: 0.8161 (m100) cc_final: 0.7121 (m100)
REVERT: A  222 ARG cc_start: 0.8685 (mtt-85) cc_final: 0.8426 (mtt-85)
REVERT: A  242 VAL cc_start: 0.9286 (p) cc_final: 0.8853 (p)
REVERT: A  262 MET cc_start: 0.7997 (tmm) cc_final: 0.7097 (tmm)
REVERT: A  270 MET cc_start: 0.8067 (mtp) cc_final: 0.7796 (mtp)
REVERT: A  272 MET cc_start: 0.7903 (mmm) cc_final: 0.7427 (mmm)
REVERT: A  275 PHE cc_start: 0.8680 (m-80) cc_final: 0.8204 (m-80)
REVERT: A  282 VAL cc_start: 0.8833 (t) cc_final: 0.8188 (t)
REVERT: A  299 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7670 (ttm170)
REVERT: A  309 GLU cc_start: 0.9026 (pm20) cc_final: 0.8669 (pp20)
REVERT: A  310 ASN cc_start: 0.8808 (m-40) cc_final: 0.8023 (m-40)
REVERT: A  316 LYS cc_start: 0.8820 (tppp) cc_final: 0.8293 (tppp)
REVERT: A  332 ARG cc_start: 0.8873 (tpp80) cc_final: 0.8441 (tpt170)
REVERT: A  344 TYR cc_start: 0.8186 (t80) cc_final: 0.7790 (t80)
REVERT: A  348 TYR cc_start: 0.7905 (t80) cc_final: 0.7612 (t80)
REVERT: B  211 TRP cc_start: 0.8332 (m100) cc_final: 0.7641 (m100)
REVERT: B  222 ARG cc_start: 0.8759 (mtt-85) cc_final: 0.8253 (mtt-85)
REVERT: B  246 MET cc_start: 0.8844 (mtp) cc_final: 0.8531 (mtp)
REVERT: B  267 ASN cc_start: 0.7972 (t0) cc_final: 0.7163 (t0)
REVERT: B  275 PHE cc_start: 0.8651 (m-80) cc_final: 0.8136 (m-80)
REVERT: B  299 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7573 (ttm170)
REVERT: B  316 LYS cc_start: 0.8618 (mmtp) cc_final: 0.7919 (mmtp)
REVERT: B  322 TYR cc_start: 0.6955 (p90) cc_final: 0.6517 (p90)
REVERT: B  344 TYR cc_start: 0.8454 (t80) cc_final: 0.8116 (t80)
REVERT: C  212 LYS cc_start: 0.9327 (mttt) cc_final: 0.9113 (mmmt)
REVERT: C  217 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7920 (mt-10)
REVERT: C  218 ASP cc_start: 0.8300 (m-30) cc_final: 0.7181 (m-30)
REVERT: C  222 ARG cc_start: 0.8936 (mtt-85) cc_final: 0.8336 (mtt-85)
REVERT: C  226 ASP cc_start: 0.8803 (t0) cc_final: 0.8414 (t0)
REVERT: C  242 VAL cc_start: 0.9055 (t) cc_final: 0.8758 (t)
REVERT: C  244 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8222 (ttm110)
REVERT: C  246 MET cc_start: 0.8843 (mtp) cc_final: 0.8454 (mtp)
REVERT: C  249 ASP cc_start: 0.8558 (t70) cc_final: 0.8103 (t70)
REVERT: C  250 LEU cc_start: 0.8688 (tp) cc_final: 0.8426 (tp)
REVERT: C  262 MET cc_start: 0.7995 (tmm) cc_final: 0.7159 (tmm)
REVERT: C  270 MET cc_start: 0.8548 (ttm) cc_final: 0.8298 (ttm)
REVERT: C  272 MET cc_start: 0.7876 (mmt) cc_final: 0.7424 (mmt)
REVERT: C  275 PHE cc_start: 0.8753 (m-80) cc_final: 0.8178 (m-80)
REVERT: C  282 VAL cc_start: 0.8757 (t) cc_final: 0.7861 (t)
REVERT: C  296 ARG cc_start: 0.7680 (ttt90) cc_final: 0.7399 (ttt90)
REVERT: C  316 LYS cc_start: 0.8641 (tppp) cc_final: 0.8056 (tppp)
REVERT: C  322 TYR cc_start: 0.7194 (p90) cc_final: 0.6795 (p90)
REVERT: C  331 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8210 (ttmt)
REVERT: C  344 TYR cc_start: 0.8491 (t80) cc_final: 0.8094 (t80)
REVERT: D  212 LYS cc_start: 0.9080 (mmtm) cc_final: 0.8864 (mmmt)
REVERT: D  242 VAL cc_start: 0.9041 (t) cc_final: 0.8715 (t)
REVERT: D  244 ARG cc_start: 0.8774 (ttm170) cc_final: 0.8552 (ttm170)
REVERT: D  245 ASP cc_start: 0.8916 (m-30) cc_final: 0.8645 (m-30)
REVERT: D  262 MET cc_start: 0.7934 (tmm) cc_final: 0.7604 (tmm)
REVERT: D  276 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8074 (mtt180)
REVERT: D  309 GLU cc_start: 0.9007 (pm20) cc_final: 0.8761 (pp20)
REVERT: D  313 ARG cc_start: 0.8861 (mmp80) cc_final: 0.8279 (mmp80)
REVERT: D  316 LYS cc_start: 0.8488 (mmmm) cc_final: 0.7708 (mmmm)
REVERT: D  322 TYR cc_start: 0.6827 (p90) cc_final: 0.6565 (p90)
REVERT: D  344 TYR cc_start: 0.8556 (t80) cc_final: 0.8073 (t80)
REVERT: D  348 TYR cc_start: 0.8209 (t80) cc_final: 0.7963 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2736
  time to fit residues: 63.5287
Evaluate side-chains
  200 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0970
   chunk 23 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.8178

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

Flipped N/Q/H residues before XYZ refinement:
A 267 ASN
B 231 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN
** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.095124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.080566 restraints weight = 13009.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.084054 restraints weight = 6692.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.086445 restraints weight = 4080.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.7900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4964  Z= 0.163
  Angle     :  0.518   5.985   6684  Z= 0.302
  Chirality :  0.039   0.136    704
  Planarity :  0.003   0.022    888
  Dihedral  :  3.761  19.313    668
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  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:  3.11 (0.36), residues: 580
  helix:  2.76 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.28 (0.58), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D 211 
 PHE   0.007   0.001   PHE D 350 
 TYR   0.016   0.001   TYR A 314 
 ARG   0.004   0.000   ARG B 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 TRP cc_start: 0.8192 (m100) cc_final: 0.7130 (m100)
REVERT: A  213 LYS cc_start: 0.8986 (mttt) cc_final: 0.8623 (mttt)
REVERT: A  222 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.8475 (mtt-85)
REVERT: A  242 VAL cc_start: 0.9282 (p) cc_final: 0.8865 (p)
REVERT: A  262 MET cc_start: 0.8044 (tmm) cc_final: 0.7096 (tmm)
REVERT: A  270 MET cc_start: 0.8161 (mtp) cc_final: 0.7916 (mtp)
REVERT: A  272 MET cc_start: 0.7941 (mmm) cc_final: 0.7452 (mmm)
REVERT: A  275 PHE cc_start: 0.8652 (m-80) cc_final: 0.8217 (m-80)
REVERT: A  282 VAL cc_start: 0.8755 (t) cc_final: 0.8113 (t)
REVERT: A  299 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7705 (ttm170)
REVERT: A  309 GLU cc_start: 0.9034 (pm20) cc_final: 0.8529 (pp20)
REVERT: A  310 ASN cc_start: 0.8820 (m-40) cc_final: 0.7693 (m-40)
REVERT: A  313 ARG cc_start: 0.8939 (mtp180) cc_final: 0.8538 (mtp180)
REVERT: A  314 TYR cc_start: 0.8250 (m-10) cc_final: 0.8000 (m-10)
REVERT: A  316 LYS cc_start: 0.8816 (tppp) cc_final: 0.8304 (tppp)
REVERT: A  332 ARG cc_start: 0.8887 (tpp80) cc_final: 0.8460 (tpt170)
REVERT: A  344 TYR cc_start: 0.8242 (t80) cc_final: 0.7863 (t80)
REVERT: A  348 TYR cc_start: 0.7920 (t80) cc_final: 0.7612 (t80)
REVERT: B  211 TRP cc_start: 0.8323 (m100) cc_final: 0.7636 (m100)
REVERT: B  217 GLU cc_start: 0.7660 (pp20) cc_final: 0.7416 (pp20)
REVERT: B  222 ARG cc_start: 0.8772 (mtt-85) cc_final: 0.8307 (mtt-85)
REVERT: B  246 MET cc_start: 0.8859 (mtp) cc_final: 0.8539 (mtp)
REVERT: B  269 ASN cc_start: 0.9024 (m-40) cc_final: 0.8815 (m-40)
REVERT: B  275 PHE cc_start: 0.8660 (m-80) cc_final: 0.8162 (m-80)
REVERT: B  299 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7579 (ttm170)
REVERT: B  316 LYS cc_start: 0.8618 (mmtp) cc_final: 0.7899 (mmtp)
REVERT: B  322 TYR cc_start: 0.7067 (p90) cc_final: 0.6692 (p90)
REVERT: B  331 LYS cc_start: 0.9170 (mttt) cc_final: 0.8161 (ttmt)
REVERT: B  344 TYR cc_start: 0.8422 (t80) cc_final: 0.8096 (t80)
REVERT: C  212 LYS cc_start: 0.9341 (mttt) cc_final: 0.9119 (mmmt)
REVERT: C  217 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7996 (mt-10)
REVERT: C  218 ASP cc_start: 0.8376 (m-30) cc_final: 0.7328 (m-30)
REVERT: C  222 ARG cc_start: 0.8963 (mtt-85) cc_final: 0.8386 (mtt-85)
REVERT: C  242 VAL cc_start: 0.9036 (t) cc_final: 0.8764 (t)
REVERT: C  246 MET cc_start: 0.8842 (mtp) cc_final: 0.8432 (mtp)
REVERT: C  249 ASP cc_start: 0.8558 (t70) cc_final: 0.8123 (t70)
REVERT: C  250 LEU cc_start: 0.8703 (tp) cc_final: 0.8436 (tp)
REVERT: C  262 MET cc_start: 0.8022 (tmm) cc_final: 0.7180 (tmm)
REVERT: C  272 MET cc_start: 0.7909 (mmt) cc_final: 0.7510 (mmt)
REVERT: C  275 PHE cc_start: 0.8776 (m-80) cc_final: 0.8257 (m-80)
REVERT: C  282 VAL cc_start: 0.8733 (t) cc_final: 0.7769 (t)
REVERT: C  316 LYS cc_start: 0.8629 (tppp) cc_final: 0.8024 (tppp)
REVERT: C  322 TYR cc_start: 0.7127 (p90) cc_final: 0.6675 (p90)
REVERT: C  331 LYS cc_start: 0.9075 (mtpt) cc_final: 0.8136 (ttmt)
REVERT: C  344 TYR cc_start: 0.8493 (t80) cc_final: 0.8096 (t80)
REVERT: D  212 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8938 (mmmt)
REVERT: D  242 VAL cc_start: 0.9042 (t) cc_final: 0.8724 (t)
REVERT: D  244 ARG cc_start: 0.8774 (ttm170) cc_final: 0.8515 (ttm170)
REVERT: D  245 ASP cc_start: 0.8920 (m-30) cc_final: 0.8635 (m-30)
REVERT: D  262 MET cc_start: 0.7942 (tmm) cc_final: 0.7630 (tmm)
REVERT: D  276 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8119 (mtt180)
REVERT: D  310 ASN cc_start: 0.9011 (m110) cc_final: 0.8507 (m-40)
REVERT: D  313 ARG cc_start: 0.8836 (mmp80) cc_final: 0.8634 (mtm-85)
REVERT: D  316 LYS cc_start: 0.8445 (mmmm) cc_final: 0.7744 (mmmm)
REVERT: D  322 TYR cc_start: 0.6838 (p90) cc_final: 0.6554 (p90)
REVERT: D  344 TYR cc_start: 0.8562 (t80) cc_final: 0.8093 (t80)
REVERT: D  348 TYR cc_start: 0.8213 (t80) cc_final: 0.7951 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.2816
  time to fit residues: 65.6553
Evaluate side-chains
  198 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:    0.0060
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0870
   chunk 0 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 ASN
C 231 ASN
** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.096956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.082300 restraints weight = 12726.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.085803 restraints weight = 6593.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.088218 restraints weight = 4050.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.8008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4964  Z= 0.146
  Angle     :  0.540   6.240   6684  Z= 0.311
  Chirality :  0.040   0.133    704
  Planarity :  0.003   0.022    888
  Dihedral  :  3.696  19.324    668
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  3.14 (0.36), residues: 580
  helix:  2.80 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.24 (0.58), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 211 
 PHE   0.004   0.001   PHE B 350 
 TYR   0.011   0.001   TYR A 314 
 ARG   0.005   0.000   ARG A 255 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 TRP cc_start: 0.8190 (m100) cc_final: 0.7147 (m100)
REVERT: A  213 LYS cc_start: 0.8898 (mttt) cc_final: 0.8581 (mttt)
REVERT: A  222 ARG cc_start: 0.8696 (mtt-85) cc_final: 0.8441 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8458 (mm-30)
REVERT: A  242 VAL cc_start: 0.9277 (p) cc_final: 0.8859 (p)
REVERT: A  262 MET cc_start: 0.8008 (tmm) cc_final: 0.7048 (tmm)
REVERT: A  270 MET cc_start: 0.8111 (mtp) cc_final: 0.7858 (mtp)
REVERT: A  272 MET cc_start: 0.7981 (mmm) cc_final: 0.7438 (mmm)
REVERT: A  275 PHE cc_start: 0.8627 (m-80) cc_final: 0.8194 (m-80)
REVERT: A  282 VAL cc_start: 0.8748 (t) cc_final: 0.8090 (t)
REVERT: A  299 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7700 (ttm170)
REVERT: A  309 GLU cc_start: 0.9040 (pm20) cc_final: 0.8512 (pp20)
REVERT: A  310 ASN cc_start: 0.8787 (m-40) cc_final: 0.7639 (m-40)
REVERT: A  313 ARG cc_start: 0.8948 (mtp180) cc_final: 0.8548 (mtp180)
REVERT: A  316 LYS cc_start: 0.8761 (tppp) cc_final: 0.8266 (tppp)
REVERT: A  332 ARG cc_start: 0.8873 (tpp80) cc_final: 0.8448 (tpt170)
REVERT: A  344 TYR cc_start: 0.8254 (t80) cc_final: 0.7874 (t80)
REVERT: A  348 TYR cc_start: 0.7933 (t80) cc_final: 0.7606 (t80)
REVERT: B  211 TRP cc_start: 0.8290 (m100) cc_final: 0.7513 (m100)
REVERT: B  222 ARG cc_start: 0.8769 (mtt-85) cc_final: 0.8315 (mtt-85)
REVERT: B  246 MET cc_start: 0.8863 (mtp) cc_final: 0.8539 (mtp)
REVERT: B  267 ASN cc_start: 0.7983 (t0) cc_final: 0.7204 (t0)
REVERT: B  269 ASN cc_start: 0.8998 (m-40) cc_final: 0.8782 (m-40)
REVERT: B  270 MET cc_start: 0.8227 (mtp) cc_final: 0.7711 (mtp)
REVERT: B  275 PHE cc_start: 0.8664 (m-80) cc_final: 0.8169 (m-80)
REVERT: B  299 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7533 (ttm170)
REVERT: B  316 LYS cc_start: 0.8549 (mmtp) cc_final: 0.7801 (mmtp)
REVERT: B  322 TYR cc_start: 0.7047 (p90) cc_final: 0.6688 (p90)
REVERT: B  331 LYS cc_start: 0.9135 (mttt) cc_final: 0.8146 (ttmt)
REVERT: B  344 TYR cc_start: 0.8442 (t80) cc_final: 0.8079 (t80)
REVERT: C  211 TRP cc_start: 0.8326 (m100) cc_final: 0.7985 (m100)
REVERT: C  212 LYS cc_start: 0.9340 (mttt) cc_final: 0.9132 (mmmt)
REVERT: C  217 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8008 (mt-10)
REVERT: C  218 ASP cc_start: 0.8348 (m-30) cc_final: 0.7278 (m-30)
REVERT: C  222 ARG cc_start: 0.8985 (mtt-85) cc_final: 0.8351 (mtt-85)
REVERT: C  242 VAL cc_start: 0.9037 (t) cc_final: 0.8745 (t)
REVERT: C  246 MET cc_start: 0.8832 (mtp) cc_final: 0.8435 (mtp)
REVERT: C  249 ASP cc_start: 0.8554 (t70) cc_final: 0.8118 (t70)
REVERT: C  250 LEU cc_start: 0.8694 (tp) cc_final: 0.8427 (tp)
REVERT: C  262 MET cc_start: 0.7977 (tmm) cc_final: 0.7125 (tmm)
REVERT: C  272 MET cc_start: 0.7917 (mmt) cc_final: 0.7453 (mmt)
REVERT: C  275 PHE cc_start: 0.8772 (m-80) cc_final: 0.8279 (m-80)
REVERT: C  282 VAL cc_start: 0.8731 (t) cc_final: 0.7760 (t)
REVERT: C  302 ASP cc_start: 0.8932 (t0) cc_final: 0.8719 (t0)
REVERT: C  316 LYS cc_start: 0.8611 (tppp) cc_final: 0.8008 (tppp)
REVERT: C  322 TYR cc_start: 0.7105 (p90) cc_final: 0.6855 (p90)
REVERT: C  331 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8204 (ttmt)
REVERT: C  344 TYR cc_start: 0.8463 (t80) cc_final: 0.8077 (t80)
REVERT: D  212 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8920 (mmmt)
REVERT: D  242 VAL cc_start: 0.9040 (t) cc_final: 0.8709 (t)
REVERT: D  245 ASP cc_start: 0.8929 (m-30) cc_final: 0.8658 (m-30)
REVERT: D  262 MET cc_start: 0.7910 (tmm) cc_final: 0.7602 (tmm)
REVERT: D  269 ASN cc_start: 0.9139 (m-40) cc_final: 0.8927 (m-40)
REVERT: D  309 GLU cc_start: 0.9002 (pm20) cc_final: 0.8650 (pp20)
REVERT: D  316 LYS cc_start: 0.8411 (mmmm) cc_final: 0.7662 (mmmm)
REVERT: D  322 TYR cc_start: 0.6802 (p90) cc_final: 0.6520 (p90)
REVERT: D  344 TYR cc_start: 0.8544 (t80) cc_final: 0.8080 (t80)
REVERT: D  348 TYR cc_start: 0.8255 (t80) cc_final: 0.7988 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.2745
  time to fit residues: 62.8647
Evaluate side-chains
  194 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN
** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.096160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.081582 restraints weight = 12973.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.085108 restraints weight = 6690.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.087494 restraints weight = 4088.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.8191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4964  Z= 0.155
  Angle     :  0.552  11.938   6684  Z= 0.314
  Chirality :  0.039   0.135    704
  Planarity :  0.003   0.022    888
  Dihedral  :  3.848  22.092    668
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.02 (0.36), residues: 580
  helix:  2.71 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.20 (0.58), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP D 211 
 PHE   0.005   0.001   PHE B 350 
 TYR   0.009   0.001   TYR C 314 
 ARG   0.005   0.000   ARG B 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 TRP cc_start: 0.8187 (m100) cc_final: 0.7134 (m100)
REVERT: A  222 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8470 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8479 (mm-30)
REVERT: A  242 VAL cc_start: 0.9276 (p) cc_final: 0.8853 (p)
REVERT: A  262 MET cc_start: 0.8024 (tmm) cc_final: 0.7072 (tmm)
REVERT: A  270 MET cc_start: 0.8135 (mtp) cc_final: 0.7887 (mtp)
REVERT: A  272 MET cc_start: 0.7966 (mmm) cc_final: 0.7436 (mmm)
REVERT: A  275 PHE cc_start: 0.8616 (m-80) cc_final: 0.8220 (m-80)
REVERT: A  282 VAL cc_start: 0.8748 (t) cc_final: 0.8073 (t)
REVERT: A  294 LEU cc_start: 0.8615 (mm) cc_final: 0.8404 (mm)
REVERT: A  299 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7654 (ttm170)
REVERT: A  309 GLU cc_start: 0.9056 (pm20) cc_final: 0.8529 (pp20)
REVERT: A  310 ASN cc_start: 0.8802 (m-40) cc_final: 0.7635 (m-40)
REVERT: A  313 ARG cc_start: 0.8992 (mtp180) cc_final: 0.8579 (mtp180)
REVERT: A  316 LYS cc_start: 0.8679 (tppp) cc_final: 0.8139 (tppp)
REVERT: A  332 ARG cc_start: 0.8841 (tpp80) cc_final: 0.8423 (tpt170)
REVERT: A  344 TYR cc_start: 0.8256 (t80) cc_final: 0.7877 (t80)
REVERT: A  348 TYR cc_start: 0.7942 (t80) cc_final: 0.7615 (t80)
REVERT: B  211 TRP cc_start: 0.8286 (m100) cc_final: 0.7547 (m100)
REVERT: B  246 MET cc_start: 0.8862 (mtp) cc_final: 0.8536 (mtp)
REVERT: B  267 ASN cc_start: 0.8032 (t0) cc_final: 0.7236 (t0)
REVERT: B  269 ASN cc_start: 0.9012 (m-40) cc_final: 0.8809 (m-40)
REVERT: B  270 MET cc_start: 0.8262 (mtp) cc_final: 0.7750 (mtp)
REVERT: B  275 PHE cc_start: 0.8660 (m-80) cc_final: 0.8165 (m-80)
REVERT: B  299 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7492 (ttm170)
REVERT: B  316 LYS cc_start: 0.8510 (mmtp) cc_final: 0.7768 (mmtp)
REVERT: B  322 TYR cc_start: 0.7068 (p90) cc_final: 0.6723 (p90)
REVERT: B  331 LYS cc_start: 0.9190 (mttt) cc_final: 0.8186 (ttmt)
REVERT: B  344 TYR cc_start: 0.8420 (t80) cc_final: 0.8061 (t80)
REVERT: C  211 TRP cc_start: 0.8332 (m100) cc_final: 0.7992 (m100)
REVERT: C  212 LYS cc_start: 0.9349 (mttt) cc_final: 0.9147 (mmmt)
REVERT: C  217 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7982 (mt-10)
REVERT: C  218 ASP cc_start: 0.8353 (m-30) cc_final: 0.7169 (m-30)
REVERT: C  222 ARG cc_start: 0.8953 (mtt-85) cc_final: 0.8242 (mtt-85)
REVERT: C  242 VAL cc_start: 0.9035 (t) cc_final: 0.8746 (t)
REVERT: C  246 MET cc_start: 0.8834 (mtp) cc_final: 0.8464 (mtp)
REVERT: C  249 ASP cc_start: 0.8577 (t70) cc_final: 0.8148 (t70)
REVERT: C  250 LEU cc_start: 0.8707 (tp) cc_final: 0.8438 (tp)
REVERT: C  257 VAL cc_start: 0.9039 (t) cc_final: 0.8747 (t)
REVERT: C  262 MET cc_start: 0.7961 (tmm) cc_final: 0.7128 (tmm)
REVERT: C  272 MET cc_start: 0.7934 (mmt) cc_final: 0.7528 (mmt)
REVERT: C  275 PHE cc_start: 0.8762 (m-80) cc_final: 0.8275 (m-80)
REVERT: C  282 VAL cc_start: 0.8741 (t) cc_final: 0.7791 (t)
REVERT: C  316 LYS cc_start: 0.8615 (tppp) cc_final: 0.8008 (tppp)
REVERT: C  322 TYR cc_start: 0.7063 (p90) cc_final: 0.6703 (p90)
REVERT: C  331 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8183 (ttmt)
REVERT: C  344 TYR cc_start: 0.8477 (t80) cc_final: 0.8092 (t80)
REVERT: D  242 VAL cc_start: 0.9037 (t) cc_final: 0.8711 (t)
REVERT: D  245 ASP cc_start: 0.8943 (m-30) cc_final: 0.8674 (m-30)
REVERT: D  262 MET cc_start: 0.7928 (tmm) cc_final: 0.7648 (tmm)
REVERT: D  309 GLU cc_start: 0.9003 (pm20) cc_final: 0.8644 (pp20)
REVERT: D  316 LYS cc_start: 0.8408 (mmmm) cc_final: 0.7652 (mmmm)
REVERT: D  322 TYR cc_start: 0.6704 (p90) cc_final: 0.6418 (p90)
REVERT: D  344 TYR cc_start: 0.8552 (t80) cc_final: 0.8080 (t80)
REVERT: D  348 TYR cc_start: 0.8247 (t80) cc_final: 0.7991 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2609
  time to fit residues: 58.6109
Evaluate side-chains
  189 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0770
   chunk 34 optimal weight:    0.1980
   chunk 35 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0770
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.097742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.082737 restraints weight = 12903.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.086272 restraints weight = 6709.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.088727 restraints weight = 4132.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.8280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4964  Z= 0.137
  Angle     :  0.549  11.918   6684  Z= 0.309
  Chirality :  0.039   0.132    704
  Planarity :  0.003   0.023    888
  Dihedral  :  3.779  24.610    668
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  3.13 (0.36), residues: 580
  helix:  2.82 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.16 (0.58), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP C 221 
 PHE   0.004   0.000   PHE C 350 
 TYR   0.006   0.001   TYR C 314 
 ARG   0.006   0.000   ARG A 255 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2118.25 seconds
wall clock time: 38 minutes 35.04 seconds (2315.04 seconds total)