Starting phenix.real_space_refine
on Thu Mar  6 04:27:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ja6_61291/03_2025/9ja6_61291.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ja6_61291/03_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_61291/03_2025/9ja6_61291.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ja6_61291/03_2025/9ja6_61291.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ja6_61291/03_2025/9ja6_61291.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ja6_61291/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.78, 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: 1.24
  Conformation dependent library (CDL) restraints added in 531.8 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: 0.48
  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: 1.14

  Time building geometry restraints manager: 1.46 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: 0.02
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:             2.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.880
  Find NCS groups from input model:        0.180
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.010
  Internal consistency checks:             0.000
  Total:   22.030
-------------------------------------------------------------------------------
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  : 0.555 
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: 72.9182
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  : 0.537 
-------------------------------------------------------------------------------
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 = 37)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.087608 restraints weight = 12630.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.091260 restraints weight = 7032.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.093898 restraints weight = 4556.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
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  : 0.565 
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: 0.7938 (mmm) cc_final: 0.7727 (mmm)
REVERT: A  213 LYS cc_start: 0.9067 (mttt) cc_final: 0.8747 (mttt)
REVERT: A  220 GLU cc_start: 0.7974 (mp0) cc_final: 0.7473 (mp0)
REVERT: A  222 ARG cc_start: 0.8631 (mtt-85) cc_final: 0.7739 (mtp85)
REVERT: A  247 ARG cc_start: 0.8941 (ttm170) cc_final: 0.8681 (ttm170)
REVERT: A  262 MET cc_start: 0.7755 (tmm) cc_final: 0.7290 (tmm)
REVERT: A  272 MET cc_start: 0.8401 (mmt) cc_final: 0.7980 (mmt)
REVERT: A  275 PHE cc_start: 0.8636 (m-80) cc_final: 0.8245 (m-80)
REVERT: A  282 VAL cc_start: 0.8967 (t) cc_final: 0.8711 (p)
REVERT: A  299 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7633 (ttm170)
REVERT: A  309 GLU cc_start: 0.8723 (pm20) cc_final: 0.8421 (pp20)
REVERT: A  316 LYS cc_start: 0.8908 (tppp) cc_final: 0.8470 (mttt)
REVERT: A  344 TYR cc_start: 0.7830 (t80) cc_final: 0.7628 (t80)
REVERT: B  208 MET cc_start: 0.7972 (mmm) cc_final: 0.7510 (mmm)
REVERT: B  217 GLU cc_start: 0.7526 (pp20) cc_final: 0.7296 (pp20)
REVERT: B  218 ASP cc_start: 0.7690 (m-30) cc_final: 0.6513 (m-30)
REVERT: B  222 ARG cc_start: 0.8754 (mtt-85) cc_final: 0.8500 (mtt-85)
REVERT: B  227 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8289 (mm-30)
REVERT: B  246 MET cc_start: 0.8931 (mtp) cc_final: 0.8431 (mtp)
REVERT: B  249 ASP cc_start: 0.8587 (t70) cc_final: 0.8115 (t0)
REVERT: B  270 MET cc_start: 0.8074 (mtp) cc_final: 0.7585 (mtp)
REVERT: B  275 PHE cc_start: 0.8757 (m-80) cc_final: 0.8155 (m-80)
REVERT: B  299 ARG cc_start: 0.8155 (ttm170) cc_final: 0.7826 (ttm170)
REVERT: B  304 ASP cc_start: 0.7170 (t0) cc_final: 0.6882 (t0)
REVERT: B  316 LYS cc_start: 0.8892 (mmtp) cc_final: 0.8383 (mmtp)
REVERT: B  322 TYR cc_start: 0.6054 (p90) cc_final: 0.5714 (p90)
REVERT: B  344 TYR cc_start: 0.8454 (t80) cc_final: 0.8232 (t80)
REVERT: C  211 TRP cc_start: 0.8250 (m100) cc_final: 0.7852 (m100)
REVERT: C  212 LYS cc_start: 0.9256 (mttt) cc_final: 0.8914 (mmmt)
REVERT: C  217 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7949 (mt-10)
REVERT: C  222 ARG cc_start: 0.8981 (mtt-85) cc_final: 0.8427 (mtt-85)
REVERT: C  226 ASP cc_start: 0.8514 (t0) cc_final: 0.8264 (t0)
REVERT: C  227 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8468 (mm-30)
REVERT: C  246 MET cc_start: 0.8764 (mtp) cc_final: 0.8299 (mtp)
REVERT: C  248 ASN cc_start: 0.9055 (m-40) cc_final: 0.8820 (m-40)
REVERT: C  249 ASP cc_start: 0.8555 (t70) cc_final: 0.8189 (t70)
REVERT: C  260 MET cc_start: 0.7646 (ttp) cc_final: 0.7438 (ttp)
REVERT: C  262 MET cc_start: 0.8037 (tmm) cc_final: 0.7231 (tmm)
REVERT: C  275 PHE cc_start: 0.8739 (m-80) cc_final: 0.8201 (m-80)
REVERT: C  282 VAL cc_start: 0.8905 (t) cc_final: 0.8010 (p)
REVERT: C  296 ARG cc_start: 0.7776 (ttt90) cc_final: 0.7447 (ttt90)
REVERT: C  304 ASP cc_start: 0.6791 (t0) cc_final: 0.5901 (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: 0.8109 (t80) cc_final: 0.7684 (t80)
REVERT: D  212 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8636 (mmmt)
REVERT: D  242 VAL cc_start: 0.8970 (t) cc_final: 0.8757 (t)
REVERT: D  245 ASP cc_start: 0.8872 (m-30) cc_final: 0.8565 (m-30)
REVERT: D  262 MET cc_start: 0.8025 (tmm) cc_final: 0.7641 (tmm)
REVERT: D  282 VAL cc_start: 0.8901 (t) cc_final: 0.8697 (p)
REVERT: D  331 LYS cc_start: 0.8639 (mttt) cc_final: 0.8368 (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: 0.2207
  time to fit residues: 59.2059
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  : 0.522 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3646 r_free = 0.3646 target = 0.097462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.082274 restraints weight = 12926.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.085921 restraints weight = 6743.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.088334 restraints weight = 4164.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.5597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4964  Z= 0.210
  Angle     :  0.557   6.133   6684  Z= 0.323
  Chirality :  0.039   0.149    704
  Planarity :  0.004   0.039    888
  Dihedral  :  4.027  17.874    668
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  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:  2.24 (0.35), residues: 580
  helix:  2.06 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.10 (0.56), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP D 211 
 PHE   0.010   0.001   PHE A 284 
 TYR   0.009   0.001   TYR C 314 
 ARG   0.004   0.000   ARG C 255 

*********************** 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
  225 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  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: symmetry clash
   revert: symmetry clash
REVERT: A  208 MET cc_start: 0.8143 (mmm) cc_final: 0.7883 (mmm)
REVERT: A  213 LYS cc_start: 0.9012 (mttt) cc_final: 0.8665 (mttt)
REVERT: A  222 ARG cc_start: 0.8701 (mtt-85) cc_final: 0.7796 (mtp85)
REVERT: A  227 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8282 (mm-30)
REVERT: A  262 MET cc_start: 0.7957 (tmm) cc_final: 0.7377 (tmm)
REVERT: A  270 MET cc_start: 0.8210 (mtp) cc_final: 0.7639 (mtp)
REVERT: A  272 MET cc_start: 0.8293 (mmt) cc_final: 0.8086 (mmp)
REVERT: A  275 PHE cc_start: 0.8776 (m-80) cc_final: 0.8249 (m-80)
REVERT: A  282 VAL cc_start: 0.8822 (t) cc_final: 0.8512 (p)
REVERT: A  299 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7593 (ttm170)
REVERT: A  309 GLU cc_start: 0.8834 (pm20) cc_final: 0.8577 (pp20)
REVERT: A  316 LYS cc_start: 0.8953 (tppp) cc_final: 0.8571 (tppp)
REVERT: A  344 TYR cc_start: 0.7982 (t80) cc_final: 0.7730 (t80)
REVERT: B  208 MET cc_start: 0.8213 (mmm) cc_final: 0.7722 (mmm)
REVERT: B  211 TRP cc_start: 0.8305 (m100) cc_final: 0.7535 (m100)
REVERT: B  213 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8583 (mtmm)
REVERT: B  222 ARG cc_start: 0.8919 (mtt-85) cc_final: 0.8268 (mtt-85)
REVERT: B  246 MET cc_start: 0.8952 (mtp) cc_final: 0.8594 (mtp)
REVERT: B  249 ASP cc_start: 0.8643 (t70) cc_final: 0.8190 (t0)
REVERT: B  268 ASN cc_start: 0.8309 (m-40) cc_final: 0.7999 (m-40)
REVERT: B  275 PHE cc_start: 0.8707 (m-80) cc_final: 0.8122 (m-80)
REVERT: B  282 VAL cc_start: 0.8813 (t) cc_final: 0.8428 (p)
REVERT: B  299 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7732 (ttm170)
REVERT: B  314 TYR cc_start: 0.8478 (m-10) cc_final: 0.8269 (m-10)
REVERT: B  316 LYS cc_start: 0.8822 (mmtp) cc_final: 0.8254 (mmtp)
REVERT: B  331 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8067 (ttmt)
REVERT: B  344 TYR cc_start: 0.8442 (t80) cc_final: 0.8177 (t80)
REVERT: C  212 LYS cc_start: 0.9314 (mttt) cc_final: 0.9001 (mmmt)
REVERT: C  217 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7976 (mt-10)
REVERT: C  222 ARG cc_start: 0.8983 (mtt-85) cc_final: 0.8520 (mtt-85)
REVERT: C  226 ASP cc_start: 0.8632 (t0) cc_final: 0.8314 (t0)
REVERT: C  227 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8516 (mm-30)
REVERT: C  246 MET cc_start: 0.9010 (mtp) cc_final: 0.8596 (mtp)
REVERT: C  249 ASP cc_start: 0.8615 (t70) cc_final: 0.8248 (t70)
REVERT: C  250 LEU cc_start: 0.8673 (tp) cc_final: 0.8228 (tp)
REVERT: C  262 MET cc_start: 0.8033 (tmm) cc_final: 0.7236 (tmm)
REVERT: C  270 MET cc_start: 0.8583 (ttm) cc_final: 0.8066 (tpp)
REVERT: C  275 PHE cc_start: 0.8784 (m-80) cc_final: 0.8189 (m-80)
REVERT: C  282 VAL cc_start: 0.8764 (t) cc_final: 0.7745 (p)
REVERT: C  296 ARG cc_start: 0.7776 (ttt90) cc_final: 0.7283 (ttt90)
REVERT: C  304 ASP cc_start: 0.6881 (t0) cc_final: 0.5998 (t0)
REVERT: C  309 GLU cc_start: 0.8601 (pp20) cc_final: 0.8267 (pp20)
REVERT: C  310 ASN cc_start: 0.8905 (m110) cc_final: 0.8676 (m110)
REVERT: C  316 LYS cc_start: 0.8796 (tppp) cc_final: 0.8409 (tppp)
REVERT: C  331 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8232 (tttt)
REVERT: C  344 TYR cc_start: 0.8539 (t80) cc_final: 0.8145 (t80)
REVERT: D  212 LYS cc_start: 0.9023 (mmtm) cc_final: 0.8709 (mmmt)
REVERT: D  218 ASP cc_start: 0.7736 (m-30) cc_final: 0.7271 (m-30)
REVERT: D  242 VAL cc_start: 0.9011 (t) cc_final: 0.8764 (t)
REVERT: D  244 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8482 (ttm170)
REVERT: D  245 ASP cc_start: 0.8907 (m-30) cc_final: 0.8590 (m-30)
REVERT: D  249 ASP cc_start: 0.8652 (t70) cc_final: 0.8016 (t70)
REVERT: D  262 MET cc_start: 0.7991 (tmm) cc_final: 0.7601 (tmm)
REVERT: D  266 ARG cc_start: 0.8314 (ttp-170) cc_final: 0.8045 (ttp80)
REVERT: D  268 ASN cc_start: 0.8418 (m-40) cc_final: 0.8196 (m-40)
REVERT: D  275 PHE cc_start: 0.8802 (m-10) cc_final: 0.8372 (m-10)
REVERT: D  282 VAL cc_start: 0.8772 (t) cc_final: 0.8488 (p)
REVERT: D  304 ASP cc_start: 0.7127 (t0) cc_final: 0.6112 (t0)
REVERT: D  309 GLU cc_start: 0.8906 (pm20) cc_final: 0.8454 (pp20)
REVERT: D  313 ARG cc_start: 0.8916 (mmp80) cc_final: 0.8522 (mmp80)
REVERT: D  316 LYS cc_start: 0.8694 (mmmm) cc_final: 0.7904 (mmmm)
REVERT: D  327 GLN cc_start: 0.6814 (mp10) cc_final: 0.6511 (mp10)
REVERT: D  331 LYS cc_start: 0.8749 (mttt) cc_final: 0.8074 (ttmt)
REVERT: D  344 TYR cc_start: 0.8562 (t80) cc_final: 0.8322 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.2493
  time to fit residues: 65.6531
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  : 0.578 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.8584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.097762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.082743 restraints weight = 12920.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.086399 restraints weight = 6549.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.088894 restraints weight = 3964.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.6194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4964  Z= 0.165
  Angle     :  0.494   5.339   6684  Z= 0.286
  Chirality :  0.039   0.138    704
  Planarity :  0.004   0.030    888
  Dihedral  :  3.795  19.783    668
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.43
  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:  2.88 (0.36), residues: 580
  helix:  2.56 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.28 (0.57), 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   0.010   0.001   TYR C 314 
 ARG   0.002   0.000   ARG C 255 

*********************** 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
  208 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.499 
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: 0.7917 (mmm) cc_final: 0.7642 (mmm)
REVERT: A  213 LYS cc_start: 0.8994 (mttt) cc_final: 0.8621 (mttt)
REVERT: A  222 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8234 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8260 (mm-30)
REVERT: A  242 VAL cc_start: 0.9211 (p) cc_final: 0.8853 (p)
REVERT: A  262 MET cc_start: 0.7907 (tmm) cc_final: 0.7343 (tmm)
REVERT: A  270 MET cc_start: 0.8249 (mtp) cc_final: 0.8000 (mtp)
REVERT: A  272 MET cc_start: 0.7780 (mmm) cc_final: 0.7373 (mmm)
REVERT: A  275 PHE cc_start: 0.8707 (m-80) cc_final: 0.8201 (m-80)
REVERT: A  299 ARG cc_start: 0.7755 (ttm170) cc_final: 0.7551 (ttm170)
REVERT: A  309 GLU cc_start: 0.8887 (pm20) cc_final: 0.8614 (pp20)
REVERT: A  316 LYS cc_start: 0.8953 (tppp) cc_final: 0.8543 (tppp)
REVERT: A  344 TYR cc_start: 0.7984 (t80) cc_final: 0.7720 (t80)
REVERT: B  208 MET cc_start: 0.8082 (mmm) cc_final: 0.7631 (mmm)
REVERT: B  211 TRP cc_start: 0.8163 (m100) cc_final: 0.7530 (m100)
REVERT: B  213 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8519 (mtmm)
REVERT: B  217 GLU cc_start: 0.7499 (pp20) cc_final: 0.7050 (pp20)
REVERT: B  218 ASP cc_start: 0.7805 (m-30) cc_final: 0.6504 (m-30)
REVERT: B  222 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8157 (mtt-85)
REVERT: B  249 ASP cc_start: 0.8501 (t70) cc_final: 0.8043 (t0)
REVERT: B  268 ASN cc_start: 0.8233 (m-40) cc_final: 0.7984 (m-40)
REVERT: B  272 MET cc_start: 0.7575 (mmp) cc_final: 0.7259 (mmt)
REVERT: B  275 PHE cc_start: 0.8674 (m-80) cc_final: 0.8122 (m-80)
REVERT: B  282 VAL cc_start: 0.8824 (t) cc_final: 0.8491 (p)
REVERT: B  299 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7592 (ttm170)
REVERT: B  316 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8105 (mmtp)
REVERT: B  322 TYR cc_start: 0.6602 (p90) cc_final: 0.5838 (p90)
REVERT: B  331 LYS cc_start: 0.9175 (mttt) cc_final: 0.8121 (ttmm)
REVERT: B  332 ARG cc_start: 0.8804 (tpp-160) cc_final: 0.8559 (mmt-90)
REVERT: B  344 TYR cc_start: 0.8392 (t80) cc_final: 0.8130 (t80)
REVERT: C  212 LYS cc_start: 0.9315 (mttt) cc_final: 0.9059 (mmmt)
REVERT: C  217 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7958 (mt-10)
REVERT: C  226 ASP cc_start: 0.8550 (t0) cc_final: 0.8307 (t0)
REVERT: C  227 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8277 (mm-30)
REVERT: C  242 VAL cc_start: 0.9004 (t) cc_final: 0.8757 (t)
REVERT: C  244 ARG cc_start: 0.8624 (ttm110) cc_final: 0.8163 (ttm110)
REVERT: C  246 MET cc_start: 0.8877 (mtp) cc_final: 0.8409 (mtp)
REVERT: C  249 ASP cc_start: 0.8430 (t70) cc_final: 0.8071 (t70)
REVERT: C  262 MET cc_start: 0.8035 (tmm) cc_final: 0.7261 (tmm)
REVERT: C  275 PHE cc_start: 0.8758 (m-80) cc_final: 0.8203 (m-80)
REVERT: C  296 ARG cc_start: 0.7639 (ttt90) cc_final: 0.7284 (ttt90)
REVERT: C  304 ASP cc_start: 0.7027 (t0) cc_final: 0.6080 (t0)
REVERT: C  316 LYS cc_start: 0.8781 (tppp) cc_final: 0.8302 (tppp)
REVERT: C  322 TYR cc_start: 0.7020 (p90) cc_final: 0.6734 (p90)
REVERT: C  331 LYS cc_start: 0.9072 (mtpt) cc_final: 0.8282 (tttt)
REVERT: C  344 TYR cc_start: 0.8465 (t80) cc_final: 0.8084 (t80)
REVERT: D  212 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8800 (mmmt)
REVERT: D  218 ASP cc_start: 0.7653 (m-30) cc_final: 0.7256 (m-30)
REVERT: D  242 VAL cc_start: 0.8935 (t) cc_final: 0.8677 (t)
REVERT: D  244 ARG cc_start: 0.8735 (ttm170) cc_final: 0.8450 (ttm170)
REVERT: D  245 ASP cc_start: 0.8890 (m-30) cc_final: 0.8579 (m-30)
REVERT: D  246 MET cc_start: 0.8548 (ptp) cc_final: 0.8334 (ptp)
REVERT: D  249 ASP cc_start: 0.8510 (t70) cc_final: 0.7968 (t70)
REVERT: D  262 MET cc_start: 0.7865 (tmm) cc_final: 0.7269 (tmm)
REVERT: D  270 MET cc_start: 0.8551 (ttm) cc_final: 0.7762 (mmm)
REVERT: D  275 PHE cc_start: 0.8735 (m-10) cc_final: 0.8339 (m-10)
REVERT: D  282 VAL cc_start: 0.8882 (t) cc_final: 0.8534 (p)
REVERT: D  304 ASP cc_start: 0.7115 (t0) cc_final: 0.6861 (t0)
REVERT: D  309 GLU cc_start: 0.8958 (pm20) cc_final: 0.8420 (pp20)
REVERT: D  313 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8504 (mmp80)
REVERT: D  316 LYS cc_start: 0.8713 (mmmm) cc_final: 0.7872 (mmmm)
REVERT: D  331 LYS cc_start: 0.8907 (mttt) cc_final: 0.8139 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.3497
  time to fit residues: 85.6964
Evaluate side-chains
  205 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 6 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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**
D 269 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.097211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.082586 restraints weight = 12781.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.086137 restraints weight = 6485.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.088603 restraints weight = 3950.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.6853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4964  Z= 0.184
  Angle     :  0.514   6.491   6684  Z= 0.297
  Chirality :  0.039   0.135    704
  Planarity :  0.004   0.025    888
  Dihedral  :  3.823  16.981    668
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.57 %
    Favored  : 97.24 %
  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:  2.95 (0.35), residues: 580
  helix:  2.62 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.27 (0.56), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 211 
 PHE   0.004   0.000   PHE B 350 
 TYR   0.012   0.001   TYR A 314 
 ARG   0.008   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
  218 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 0.674 
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: A  208 MET cc_start: 0.8167 (mmm) cc_final: 0.7939 (mmm)
REVERT: A  213 LYS cc_start: 0.9048 (mttt) cc_final: 0.8666 (mttt)
REVERT: A  217 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7516 (pm20)
REVERT: A  218 ASP cc_start: 0.8001 (m-30) cc_final: 0.7254 (m-30)
REVERT: A  222 ARG cc_start: 0.8754 (mtt-85) cc_final: 0.8467 (mtt-85)
REVERT: A  241 ASP cc_start: 0.8561 (t0) cc_final: 0.8343 (t0)
REVERT: A  242 VAL cc_start: 0.9214 (p) cc_final: 0.8801 (p)
REVERT: A  249 ASP cc_start: 0.8676 (t70) cc_final: 0.8220 (t0)
REVERT: A  262 MET cc_start: 0.8056 (tmm) cc_final: 0.7587 (tmm)
REVERT: A  270 MET cc_start: 0.8248 (mtp) cc_final: 0.7998 (mtp)
REVERT: A  272 MET cc_start: 0.7851 (mmm) cc_final: 0.7398 (mmm)
REVERT: A  275 PHE cc_start: 0.8751 (m-80) cc_final: 0.8257 (m-80)
REVERT: A  299 ARG cc_start: 0.7930 (ttm170) cc_final: 0.7654 (ttm170)
REVERT: A  309 GLU cc_start: 0.8932 (pm20) cc_final: 0.8551 (pp20)
REVERT: A  310 ASN cc_start: 0.8905 (m-40) cc_final: 0.8020 (m-40)
REVERT: A  316 LYS cc_start: 0.8924 (tppp) cc_final: 0.8496 (tppp)
REVERT: A  332 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8497 (tpt170)
REVERT: B  217 GLU cc_start: 0.7552 (pp20) cc_final: 0.7068 (pp20)
REVERT: B  218 ASP cc_start: 0.7862 (m-30) cc_final: 0.6644 (m-30)
REVERT: B  222 ARG cc_start: 0.8788 (mtt-85) cc_final: 0.8294 (mtt-85)
REVERT: B  249 ASP cc_start: 0.8653 (t70) cc_final: 0.8203 (t0)
REVERT: B  272 MET cc_start: 0.7566 (mmp) cc_final: 0.7359 (mmp)
REVERT: B  275 PHE cc_start: 0.8686 (m-80) cc_final: 0.8114 (m-80)
REVERT: B  281 GLU cc_start: 0.7894 (tt0) cc_final: 0.7681 (tt0)
REVERT: B  299 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7573 (ttm170)
REVERT: B  316 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8025 (mmtp)
REVERT: B  322 TYR cc_start: 0.6845 (p90) cc_final: 0.6400 (p90)
REVERT: B  344 TYR cc_start: 0.8485 (t80) cc_final: 0.8210 (t80)
REVERT: C  212 LYS cc_start: 0.9326 (mttt) cc_final: 0.9053 (mmmt)
REVERT: C  217 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8035 (mt-10)
REVERT: C  218 ASP cc_start: 0.8361 (m-30) cc_final: 0.7249 (m-30)
REVERT: C  222 ARG cc_start: 0.8958 (mtt-85) cc_final: 0.8490 (mtt-85)
REVERT: C  242 VAL cc_start: 0.9031 (t) cc_final: 0.8778 (t)
REVERT: C  244 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8228 (ttm110)
REVERT: C  246 MET cc_start: 0.8896 (mtp) cc_final: 0.8492 (mtp)
REVERT: C  249 ASP cc_start: 0.8545 (t70) cc_final: 0.8156 (t70)
REVERT: C  250 LEU cc_start: 0.8677 (tp) cc_final: 0.8222 (tp)
REVERT: C  262 MET cc_start: 0.8038 (tmm) cc_final: 0.7201 (tmm)
REVERT: C  275 PHE cc_start: 0.8769 (m-80) cc_final: 0.8193 (m-80)
REVERT: C  282 VAL cc_start: 0.8788 (t) cc_final: 0.7843 (t)
REVERT: C  294 LEU cc_start: 0.8814 (mm) cc_final: 0.8612 (mm)
REVERT: C  296 ARG cc_start: 0.7740 (ttt90) cc_final: 0.7392 (ttt90)
REVERT: C  304 ASP cc_start: 0.6956 (t0) cc_final: 0.5340 (t0)
REVERT: C  316 LYS cc_start: 0.8740 (tppp) cc_final: 0.8238 (tppp)
REVERT: C  331 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8179 (ttmt)
REVERT: C  344 TYR cc_start: 0.8491 (t80) cc_final: 0.8117 (t80)
REVERT: C  348 TYR cc_start: 0.8211 (t80) cc_final: 0.7989 (t80)
REVERT: D  218 ASP cc_start: 0.7807 (m-30) cc_final: 0.7427 (m-30)
REVERT: D  231 ASN cc_start: 0.9035 (m110) cc_final: 0.8828 (m110)
REVERT: D  242 VAL cc_start: 0.9037 (t) cc_final: 0.8772 (t)
REVERT: D  244 ARG cc_start: 0.8757 (ttm170) cc_final: 0.8499 (ttm170)
REVERT: D  245 ASP cc_start: 0.8936 (m-30) cc_final: 0.8612 (m-30)
REVERT: D  249 ASP cc_start: 0.8614 (t70) cc_final: 0.7967 (t70)
REVERT: D  262 MET cc_start: 0.7949 (tmm) cc_final: 0.7567 (tmm)
REVERT: D  268 ASN cc_start: 0.8360 (m-40) cc_final: 0.8086 (m-40)
REVERT: D  270 MET cc_start: 0.8363 (ttm) cc_final: 0.7999 (ttm)
REVERT: D  275 PHE cc_start: 0.8743 (m-10) cc_final: 0.8376 (m-10)
REVERT: D  281 GLU cc_start: 0.8049 (tt0) cc_final: 0.7586 (tm-30)
REVERT: D  304 ASP cc_start: 0.7052 (t0) cc_final: 0.6831 (t0)
REVERT: D  309 GLU cc_start: 0.8976 (pm20) cc_final: 0.8460 (pp20)
REVERT: D  313 ARG cc_start: 0.8899 (mmp80) cc_final: 0.8482 (mmp80)
REVERT: D  316 LYS cc_start: 0.8630 (mmmm) cc_final: 0.7811 (mmmm)
REVERT: D  331 LYS cc_start: 0.8946 (mttt) cc_final: 0.8145 (ttmt)
  outliers start: 1
  outliers final: 0
  residues processed: 217
  average time/residue: 0.3220
  time to fit residues: 81.9986
Evaluate side-chains
  214 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 213
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0870
   chunk 45 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.097921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.082925 restraints weight = 12750.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.086455 restraints weight = 6646.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.088932 restraints weight = 4128.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.7102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4964  Z= 0.136
  Angle     :  0.496   5.956   6684  Z= 0.283
  Chirality :  0.038   0.131    704
  Planarity :  0.003   0.025    888
  Dihedral  :  3.637  17.625    668
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  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:  3.41 (0.36), residues: 580
  helix:  3.01 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.33 (0.55), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 211 
 PHE   0.008   0.001   PHE D 350 
 TYR   0.011   0.001   TYR C 314 
 ARG   0.004   0.000   ARG B 228 

*********************** 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
  203 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.986 
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  208 MET cc_start: 0.8158 (mmm) cc_final: 0.7950 (mmm)
REVERT: A  213 LYS cc_start: 0.8931 (mttt) cc_final: 0.8441 (mttt)
REVERT: A  217 GLU cc_start: 0.7806 (pm20) cc_final: 0.7379 (pm20)
REVERT: A  222 ARG cc_start: 0.8646 (mtt-85) cc_final: 0.8390 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8262 (mm-30)
REVERT: A  242 VAL cc_start: 0.9306 (p) cc_final: 0.8903 (p)
REVERT: A  262 MET cc_start: 0.8064 (tmm) cc_final: 0.7551 (tmm)
REVERT: A  270 MET cc_start: 0.8217 (mtp) cc_final: 0.7937 (mtp)
REVERT: A  272 MET cc_start: 0.7812 (mmm) cc_final: 0.7372 (mmm)
REVERT: A  275 PHE cc_start: 0.8739 (m-80) cc_final: 0.8257 (m-80)
REVERT: A  299 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7668 (ttm170)
REVERT: A  309 GLU cc_start: 0.8962 (pm20) cc_final: 0.8594 (pp20)
REVERT: A  310 ASN cc_start: 0.8818 (m-40) cc_final: 0.8018 (m-40)
REVERT: A  316 LYS cc_start: 0.8861 (tppp) cc_final: 0.8423 (tppp)
REVERT: A  332 ARG cc_start: 0.8857 (tpp80) cc_final: 0.8436 (tpt170)
REVERT: A  344 TYR cc_start: 0.8169 (t80) cc_final: 0.7779 (t80)
REVERT: B  222 ARG cc_start: 0.8772 (mtt-85) cc_final: 0.8231 (mtt-85)
REVERT: B  246 MET cc_start: 0.8836 (mtp) cc_final: 0.8543 (mtp)
REVERT: B  275 PHE cc_start: 0.8694 (m-80) cc_final: 0.8167 (m-80)
REVERT: B  282 VAL cc_start: 0.8751 (t) cc_final: 0.8535 (p)
REVERT: B  299 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7564 (ttm170)
REVERT: B  316 LYS cc_start: 0.8664 (mmtp) cc_final: 0.7861 (mmtp)
REVERT: B  322 TYR cc_start: 0.6814 (p90) cc_final: 0.6564 (p90)
REVERT: B  331 LYS cc_start: 0.9206 (mttt) cc_final: 0.8091 (ttmm)
REVERT: B  344 TYR cc_start: 0.8461 (t80) cc_final: 0.8177 (t80)
REVERT: C  212 LYS cc_start: 0.9309 (mttt) cc_final: 0.9054 (mmmt)
REVERT: C  217 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7958 (mt-10)
REVERT: C  218 ASP cc_start: 0.8337 (m-30) cc_final: 0.7180 (m-30)
REVERT: C  222 ARG cc_start: 0.8998 (mtt-85) cc_final: 0.8400 (mtt-85)
REVERT: C  229 LEU cc_start: 0.9204 (mt) cc_final: 0.8947 (mt)
REVERT: C  242 VAL cc_start: 0.9046 (t) cc_final: 0.8758 (t)
REVERT: C  244 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8223 (ttm110)
REVERT: C  246 MET cc_start: 0.8870 (mtp) cc_final: 0.8462 (mtp)
REVERT: C  249 ASP cc_start: 0.8507 (t70) cc_final: 0.8145 (t70)
REVERT: C  250 LEU cc_start: 0.8598 (tp) cc_final: 0.8163 (tp)
REVERT: C  262 MET cc_start: 0.7967 (tmm) cc_final: 0.7127 (tmm)
REVERT: C  275 PHE cc_start: 0.8771 (m-80) cc_final: 0.8193 (m-80)
REVERT: C  282 VAL cc_start: 0.8815 (t) cc_final: 0.7848 (t)
REVERT: C  296 ARG cc_start: 0.7670 (ttt90) cc_final: 0.7360 (ttt90)
REVERT: C  302 ASP cc_start: 0.8937 (t0) cc_final: 0.8658 (t0)
REVERT: C  304 ASP cc_start: 0.7019 (t0) cc_final: 0.5261 (t0)
REVERT: C  316 LYS cc_start: 0.8697 (tppp) cc_final: 0.8127 (tppp)
REVERT: C  322 TYR cc_start: 0.7063 (p90) cc_final: 0.6857 (p90)
REVERT: C  331 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8127 (ttmt)
REVERT: C  344 TYR cc_start: 0.8466 (t80) cc_final: 0.8049 (t80)
REVERT: C  348 TYR cc_start: 0.8155 (t80) cc_final: 0.7900 (t80)
REVERT: D  212 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8758 (mmmt)
REVERT: D  218 ASP cc_start: 0.7712 (m-30) cc_final: 0.7341 (m-30)
REVERT: D  231 ASN cc_start: 0.8981 (m110) cc_final: 0.8774 (m110)
REVERT: D  242 VAL cc_start: 0.9009 (t) cc_final: 0.8721 (t)
REVERT: D  244 ARG cc_start: 0.8762 (ttm170) cc_final: 0.8474 (ttm170)
REVERT: D  245 ASP cc_start: 0.8930 (m-30) cc_final: 0.8623 (m-30)
REVERT: D  249 ASP cc_start: 0.8616 (t70) cc_final: 0.7964 (t70)
REVERT: D  262 MET cc_start: 0.7904 (tmm) cc_final: 0.7465 (tmm)
REVERT: D  267 ASN cc_start: 0.8416 (t0) cc_final: 0.8032 (t0)
REVERT: D  270 MET cc_start: 0.8428 (ttm) cc_final: 0.8163 (ttm)
REVERT: D  275 PHE cc_start: 0.8719 (m-10) cc_final: 0.8373 (m-10)
REVERT: D  304 ASP cc_start: 0.7023 (t0) cc_final: 0.6691 (t0)
REVERT: D  309 GLU cc_start: 0.8979 (pm20) cc_final: 0.8753 (pp20)
REVERT: D  316 LYS cc_start: 0.8549 (mmmm) cc_final: 0.7828 (mmmm)
REVERT: D  331 LYS cc_start: 0.8929 (mttt) cc_final: 0.8081 (ttmt)
REVERT: D  332 ARG cc_start: 0.8557 (mmt-90) cc_final: 0.8355 (mmt-90)
REVERT: D  344 TYR cc_start: 0.8592 (t80) cc_final: 0.8100 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.3941
  time to fit residues: 92.5663
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 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 7 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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
** 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 = 0.3652 r_free = 0.3652 target = 0.097492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.082601 restraints weight = 12609.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.086099 restraints weight = 6549.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.088531 restraints weight = 4075.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.7344

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= 0.141
  Angle     :  0.500   5.685   6684  Z= 0.287
  Chirality :  0.039   0.132    704
  Planarity :  0.003   0.025    888
  Dihedral  :  3.643  21.440    668
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  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:  3.40 (0.36), residues: 580
  helix:  3.00 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.31 (0.55), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 221 
 PHE   0.006   0.001   PHE C 284 
 TYR   0.012   0.001   TYR A 314 
 ARG   0.005   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
  211 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.778 
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: A  213 LYS cc_start: 0.8935 (mttt) cc_final: 0.8585 (mttt)
REVERT: A  222 ARG cc_start: 0.8687 (mtt-85) cc_final: 0.8433 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8071 (mm-30)
REVERT: A  242 VAL cc_start: 0.9292 (p) cc_final: 0.8901 (p)
REVERT: A  262 MET cc_start: 0.8060 (tmm) cc_final: 0.7547 (tmm)
REVERT: A  270 MET cc_start: 0.8054 (mtp) cc_final: 0.7775 (mtp)
REVERT: A  272 MET cc_start: 0.7897 (mmm) cc_final: 0.7441 (mmm)
REVERT: A  275 PHE cc_start: 0.8717 (m-80) cc_final: 0.8263 (m-80)
REVERT: A  299 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7675 (ttm170)
REVERT: A  309 GLU cc_start: 0.8985 (pm20) cc_final: 0.8651 (pp20)
REVERT: A  310 ASN cc_start: 0.8801 (m-40) cc_final: 0.8032 (m-40)
REVERT: A  316 LYS cc_start: 0.8831 (tppp) cc_final: 0.8379 (tppp)
REVERT: A  332 ARG cc_start: 0.8850 (tpp80) cc_final: 0.8446 (tpt170)
REVERT: A  344 TYR cc_start: 0.8195 (t80) cc_final: 0.7791 (t80)
REVERT: B  217 GLU cc_start: 0.7625 (pp20) cc_final: 0.7082 (pp20)
REVERT: B  218 ASP cc_start: 0.7975 (m-30) cc_final: 0.6640 (m-30)
REVERT: B  222 ARG cc_start: 0.8767 (mtt-85) cc_final: 0.8244 (mtt-85)
REVERT: B  246 MET cc_start: 0.8897 (mtp) cc_final: 0.8549 (mtp)
REVERT: B  249 ASP cc_start: 0.8625 (t70) cc_final: 0.8174 (t0)
REVERT: B  267 ASN cc_start: 0.7886 (t0) cc_final: 0.7117 (t0)
REVERT: B  272 MET cc_start: 0.7524 (mmp) cc_final: 0.7308 (mmp)
REVERT: B  275 PHE cc_start: 0.8686 (m-80) cc_final: 0.8216 (m-80)
REVERT: B  282 VAL cc_start: 0.8807 (t) cc_final: 0.8549 (p)
REVERT: B  299 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7605 (ttm170)
REVERT: B  316 LYS cc_start: 0.8641 (mmtp) cc_final: 0.7931 (mmtp)
REVERT: B  322 TYR cc_start: 0.6830 (p90) cc_final: 0.6367 (p90)
REVERT: B  331 LYS cc_start: 0.9174 (mttt) cc_final: 0.8076 (ttmm)
REVERT: B  344 TYR cc_start: 0.8468 (t80) cc_final: 0.8160 (t80)
REVERT: B  352 PRO cc_start: 0.8625 (Cg_exo) cc_final: 0.8412 (Cg_endo)
REVERT: C  212 LYS cc_start: 0.9326 (mttt) cc_final: 0.9083 (mmmt)
REVERT: C  217 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8043 (mt-10)
REVERT: C  218 ASP cc_start: 0.8352 (m-30) cc_final: 0.7235 (m-30)
REVERT: C  222 ARG cc_start: 0.8984 (mtt-85) cc_final: 0.8412 (mtt-85)
REVERT: C  242 VAL cc_start: 0.9035 (t) cc_final: 0.8741 (t)
REVERT: C  244 ARG cc_start: 0.8698 (ttm110) cc_final: 0.8240 (ttm110)
REVERT: C  246 MET cc_start: 0.8872 (mtp) cc_final: 0.8451 (mtp)
REVERT: C  249 ASP cc_start: 0.8578 (t70) cc_final: 0.8118 (t70)
REVERT: C  250 LEU cc_start: 0.8666 (tp) cc_final: 0.8450 (tp)
REVERT: C  257 VAL cc_start: 0.9041 (t) cc_final: 0.8840 (t)
REVERT: C  262 MET cc_start: 0.7986 (tmm) cc_final: 0.7153 (tmm)
REVERT: C  272 MET cc_start: 0.7819 (mmt) cc_final: 0.7329 (mmt)
REVERT: C  275 PHE cc_start: 0.8762 (m-80) cc_final: 0.8205 (m-80)
REVERT: C  282 VAL cc_start: 0.8784 (t) cc_final: 0.7906 (t)
REVERT: C  296 ARG cc_start: 0.7646 (ttt90) cc_final: 0.7343 (ttt90)
REVERT: C  302 ASP cc_start: 0.8935 (t0) cc_final: 0.8660 (t0)
REVERT: C  304 ASP cc_start: 0.7155 (t0) cc_final: 0.6426 (t0)
REVERT: C  316 LYS cc_start: 0.8628 (tppp) cc_final: 0.8053 (tppp)
REVERT: C  322 TYR cc_start: 0.7124 (p90) cc_final: 0.6914 (p90)
REVERT: C  344 TYR cc_start: 0.8460 (t80) cc_final: 0.8060 (t80)
REVERT: C  348 TYR cc_start: 0.8165 (t80) cc_final: 0.7930 (t80)
REVERT: D  242 VAL cc_start: 0.9000 (t) cc_final: 0.8701 (t)
REVERT: D  244 ARG cc_start: 0.8788 (ttm170) cc_final: 0.8513 (ttm170)
REVERT: D  245 ASP cc_start: 0.8919 (m-30) cc_final: 0.8609 (m-30)
REVERT: D  262 MET cc_start: 0.7869 (tmm) cc_final: 0.7547 (tmm)
REVERT: D  276 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8031 (mtt180)
REVERT: D  281 GLU cc_start: 0.8187 (tt0) cc_final: 0.7625 (tm-30)
REVERT: D  309 GLU cc_start: 0.8976 (pm20) cc_final: 0.8743 (pp20)
REVERT: D  313 ARG cc_start: 0.8892 (mmp80) cc_final: 0.8295 (mmp80)
REVERT: D  316 LYS cc_start: 0.8505 (mmmm) cc_final: 0.7730 (mmmm)
REVERT: D  344 TYR cc_start: 0.8584 (t80) cc_final: 0.8107 (t80)
REVERT: D  348 TYR cc_start: 0.8165 (t80) cc_final: 0.7813 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.2963
  time to fit residues: 72.1910
Evaluate side-chains
  208 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 55 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 16 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:
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 = 0.3631 r_free = 0.3631 target = 0.096505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.081515 restraints weight = 12987.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.085072 restraints weight = 6751.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.087486 restraints weight = 4164.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.7659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4964  Z= 0.152
  Angle     :  0.518   5.713   6684  Z= 0.302
  Chirality :  0.040   0.137    704
  Planarity :  0.004   0.030    888
  Dihedral  :  3.743  22.222    668
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.32 (0.36), residues: 580
  helix:  2.94 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.30 (0.56), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 211 
 PHE   0.006   0.001   PHE C 350 
 TYR   0.014   0.001   TYR A 314 
 ARG   0.006   0.000   ARG C 299 

*********************** 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
  192 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.560 
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: 0.8165 (m100) cc_final: 0.7178 (m100)
REVERT: A  213 LYS cc_start: 0.8940 (mttt) cc_final: 0.8602 (mttt)
REVERT: A  222 ARG cc_start: 0.8659 (mtt-85) cc_final: 0.8438 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8152 (mm-30)
REVERT: A  242 VAL cc_start: 0.9285 (p) cc_final: 0.8861 (p)
REVERT: A  255 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.8444 (mtm-85)
REVERT: A  262 MET cc_start: 0.8062 (tmm) cc_final: 0.7580 (tmm)
REVERT: A  272 MET cc_start: 0.7899 (mmm) cc_final: 0.7415 (mmm)
REVERT: A  275 PHE cc_start: 0.8673 (m-80) cc_final: 0.8242 (m-80)
REVERT: A  294 LEU cc_start: 0.8566 (mm) cc_final: 0.8315 (mm)
REVERT: A  299 ARG cc_start: 0.7961 (ttm170) cc_final: 0.7679 (ttm170)
REVERT: A  309 GLU cc_start: 0.8987 (pm20) cc_final: 0.8500 (pp20)
REVERT: A  310 ASN cc_start: 0.8809 (m-40) cc_final: 0.7631 (m-40)
REVERT: A  313 ARG cc_start: 0.8912 (mtp180) cc_final: 0.8527 (mtp180)
REVERT: A  314 TYR cc_start: 0.8193 (m-10) cc_final: 0.7925 (m-10)
REVERT: A  316 LYS cc_start: 0.8832 (tppp) cc_final: 0.8296 (tppp)
REVERT: A  332 ARG cc_start: 0.8877 (tpp80) cc_final: 0.8472 (tpt170)
REVERT: A  344 TYR cc_start: 0.8213 (t80) cc_final: 0.7801 (t80)
REVERT: B  211 TRP cc_start: 0.8288 (m100) cc_final: 0.7637 (m100)
REVERT: B  217 GLU cc_start: 0.7671 (pp20) cc_final: 0.7407 (pp20)
REVERT: B  222 ARG cc_start: 0.8755 (mtt-85) cc_final: 0.8281 (mtt-85)
REVERT: B  246 MET cc_start: 0.8828 (mtp) cc_final: 0.8514 (mtp)
REVERT: B  272 MET cc_start: 0.7561 (mmp) cc_final: 0.7266 (mmp)
REVERT: B  275 PHE cc_start: 0.8679 (m-80) cc_final: 0.8214 (m-80)
REVERT: B  282 VAL cc_start: 0.8782 (t) cc_final: 0.8302 (p)
REVERT: B  299 ARG cc_start: 0.7802 (ttm170) cc_final: 0.7543 (ttm170)
REVERT: B  310 ASN cc_start: 0.9109 (m110) cc_final: 0.8883 (m110)
REVERT: B  316 LYS cc_start: 0.8669 (mmtp) cc_final: 0.7944 (mmtp)
REVERT: B  322 TYR cc_start: 0.6931 (p90) cc_final: 0.6517 (p90)
REVERT: B  331 LYS cc_start: 0.9116 (mttt) cc_final: 0.7994 (ttmm)
REVERT: B  344 TYR cc_start: 0.8478 (t80) cc_final: 0.8124 (t80)
REVERT: B  352 PRO cc_start: 0.8661 (Cg_exo) cc_final: 0.8452 (Cg_endo)
REVERT: C  212 LYS cc_start: 0.9321 (mttt) cc_final: 0.9112 (mmmt)
REVERT: C  217 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7978 (mt-10)
REVERT: C  218 ASP cc_start: 0.8322 (m-30) cc_final: 0.7187 (m-30)
REVERT: C  222 ARG cc_start: 0.8943 (mtt-85) cc_final: 0.8370 (mtt-85)
REVERT: C  242 VAL cc_start: 0.9038 (t) cc_final: 0.8747 (t)
REVERT: C  246 MET cc_start: 0.8814 (mtp) cc_final: 0.8401 (mtp)
REVERT: C  249 ASP cc_start: 0.8562 (t70) cc_final: 0.8119 (t70)
REVERT: C  250 LEU cc_start: 0.8666 (tp) cc_final: 0.8419 (tp)
REVERT: C  257 VAL cc_start: 0.9059 (t) cc_final: 0.8781 (t)
REVERT: C  262 MET cc_start: 0.7948 (tmm) cc_final: 0.7131 (tmm)
REVERT: C  275 PHE cc_start: 0.8776 (m-80) cc_final: 0.8271 (m-80)
REVERT: C  282 VAL cc_start: 0.8804 (t) cc_final: 0.7890 (t)
REVERT: C  302 ASP cc_start: 0.8909 (t0) cc_final: 0.8677 (t0)
REVERT: C  304 ASP cc_start: 0.7133 (t0) cc_final: 0.6372 (t0)
REVERT: C  316 LYS cc_start: 0.8635 (tppp) cc_final: 0.8029 (tppp)
REVERT: C  322 TYR cc_start: 0.7136 (p90) cc_final: 0.6865 (p90)
REVERT: C  344 TYR cc_start: 0.8455 (t80) cc_final: 0.8049 (t80)
REVERT: C  348 TYR cc_start: 0.8223 (t80) cc_final: 0.7974 (t80)
REVERT: D  212 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8913 (mmmt)
REVERT: D  231 ASN cc_start: 0.8990 (m110) cc_final: 0.8786 (m110)
REVERT: D  242 VAL cc_start: 0.9002 (t) cc_final: 0.8693 (t)
REVERT: D  245 ASP cc_start: 0.8908 (m-30) cc_final: 0.8593 (m-30)
REVERT: D  262 MET cc_start: 0.7861 (tmm) cc_final: 0.7582 (tmm)
REVERT: D  270 MET cc_start: 0.8270 (ttm) cc_final: 0.7997 (tpt)
REVERT: D  309 GLU cc_start: 0.8979 (pm20) cc_final: 0.8730 (pp20)
REVERT: D  316 LYS cc_start: 0.8471 (mmmm) cc_final: 0.7730 (mmmm)
REVERT: D  344 TYR cc_start: 0.8566 (t80) cc_final: 0.8078 (t80)
REVERT: D  348 TYR cc_start: 0.8225 (t80) cc_final: 0.7925 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2477
  time to fit residues: 55.8791
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  : 0.535 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 39 optimal weight:    0.2980
   chunk 25 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0770
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.6742

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.096584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.081838 restraints weight = 12772.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.085318 restraints weight = 6693.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.087579 restraints weight = 4131.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.7851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4964  Z= 0.151
  Angle     :  0.531   5.915   6684  Z= 0.309
  Chirality :  0.040   0.134    704
  Planarity :  0.004   0.034    888
  Dihedral  :  3.743  22.730    668
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  3.27 (0.36), residues: 580
  helix:  2.90 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.28 (0.56), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D 211 
 PHE   0.006   0.001   PHE C 350 
 TYR   0.021   0.001   TYR B 314 
 ARG   0.007   0.000   ARG C 299 

*********************** 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
  188 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.583 
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: 0.8214 (m100) cc_final: 0.7238 (m100)
REVERT: A  213 LYS cc_start: 0.8897 (mttt) cc_final: 0.8567 (mttt)
REVERT: A  222 ARG cc_start: 0.8695 (mtt-85) cc_final: 0.8453 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8427 (mm-30)
REVERT: A  242 VAL cc_start: 0.9313 (p) cc_final: 0.8903 (p)
REVERT: A  262 MET cc_start: 0.8094 (tmm) cc_final: 0.7587 (tmm)
REVERT: A  272 MET cc_start: 0.7947 (mmm) cc_final: 0.7460 (mmm)
REVERT: A  275 PHE cc_start: 0.8669 (m-80) cc_final: 0.8256 (m-80)
REVERT: A  299 ARG cc_start: 0.7960 (ttm170) cc_final: 0.7696 (ttm170)
REVERT: A  309 GLU cc_start: 0.9002 (pm20) cc_final: 0.8475 (pp20)
REVERT: A  310 ASN cc_start: 0.8793 (m-40) cc_final: 0.7618 (m-40)
REVERT: A  313 ARG cc_start: 0.8934 (mtp180) cc_final: 0.8528 (mtp180)
REVERT: A  316 LYS cc_start: 0.8780 (tppp) cc_final: 0.8255 (tppp)
REVERT: A  332 ARG cc_start: 0.8873 (tpp80) cc_final: 0.8472 (tpt170)
REVERT: A  344 TYR cc_start: 0.8247 (t80) cc_final: 0.7824 (t80)
REVERT: B  211 TRP cc_start: 0.8362 (m100) cc_final: 0.7645 (m100)
REVERT: B  222 ARG cc_start: 0.8803 (mtt-85) cc_final: 0.8355 (mtt-85)
REVERT: B  246 MET cc_start: 0.8861 (mtp) cc_final: 0.8552 (mtp)
REVERT: B  267 ASN cc_start: 0.7885 (t0) cc_final: 0.7083 (t0)
REVERT: B  275 PHE cc_start: 0.8707 (m-80) cc_final: 0.8258 (m-80)
REVERT: B  282 VAL cc_start: 0.8786 (t) cc_final: 0.8401 (p)
REVERT: B  299 ARG cc_start: 0.7871 (ttm170) cc_final: 0.7593 (ttm170)
REVERT: B  316 LYS cc_start: 0.8608 (mmtp) cc_final: 0.7892 (mmtp)
REVERT: B  322 TYR cc_start: 0.7017 (p90) cc_final: 0.6609 (p90)
REVERT: B  331 LYS cc_start: 0.9178 (mttt) cc_final: 0.8153 (ttmt)
REVERT: B  344 TYR cc_start: 0.8440 (t80) cc_final: 0.8093 (t80)
REVERT: B  352 PRO cc_start: 0.8641 (Cg_exo) cc_final: 0.8435 (Cg_endo)
REVERT: C  212 LYS cc_start: 0.9339 (mttt) cc_final: 0.9109 (mmmt)
REVERT: C  217 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7945 (mt-10)
REVERT: C  218 ASP cc_start: 0.8346 (m-30) cc_final: 0.7220 (m-30)
REVERT: C  222 ARG cc_start: 0.8981 (mtt-85) cc_final: 0.8356 (mtt-85)
REVERT: C  242 VAL cc_start: 0.9029 (t) cc_final: 0.8747 (t)
REVERT: C  246 MET cc_start: 0.8826 (mtp) cc_final: 0.8419 (mtp)
REVERT: C  249 ASP cc_start: 0.8577 (t70) cc_final: 0.8145 (t70)
REVERT: C  250 LEU cc_start: 0.8681 (tp) cc_final: 0.8431 (tp)
REVERT: C  257 VAL cc_start: 0.9055 (t) cc_final: 0.8776 (t)
REVERT: C  262 MET cc_start: 0.7978 (tmm) cc_final: 0.7154 (tmm)
REVERT: C  275 PHE cc_start: 0.8769 (m-80) cc_final: 0.8254 (m-80)
REVERT: C  282 VAL cc_start: 0.8765 (t) cc_final: 0.7859 (t)
REVERT: C  304 ASP cc_start: 0.7172 (t0) cc_final: 0.6366 (t0)
REVERT: C  316 LYS cc_start: 0.8637 (tppp) cc_final: 0.8035 (tppp)
REVERT: C  322 TYR cc_start: 0.7155 (p90) cc_final: 0.6863 (p90)
REVERT: C  344 TYR cc_start: 0.8460 (t80) cc_final: 0.8053 (t80)
REVERT: C  348 TYR cc_start: 0.8205 (t80) cc_final: 0.7946 (t80)
REVERT: D  212 LYS cc_start: 0.9117 (mmtm) cc_final: 0.8907 (mmmt)
REVERT: D  242 VAL cc_start: 0.9011 (t) cc_final: 0.8705 (t)
REVERT: D  245 ASP cc_start: 0.8926 (m-30) cc_final: 0.8615 (m-30)
REVERT: D  262 MET cc_start: 0.7854 (tmm) cc_final: 0.7560 (tmm)
REVERT: D  270 MET cc_start: 0.8379 (ttm) cc_final: 0.8069 (tpt)
REVERT: D  309 GLU cc_start: 0.8967 (pm20) cc_final: 0.8713 (pp20)
REVERT: D  316 LYS cc_start: 0.8421 (mmmm) cc_final: 0.7689 (mmmm)
REVERT: D  344 TYR cc_start: 0.8565 (t80) cc_final: 0.8094 (t80)
REVERT: D  348 TYR cc_start: 0.8224 (t80) cc_final: 0.7995 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.2594
  time to fit residues: 56.8108
Evaluate side-chains
  187 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3615 r_free = 0.3615 target = 0.095462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.080715 restraints weight = 13190.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.084209 restraints weight = 6929.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.086622 restraints weight = 4274.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.8046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4964  Z= 0.162
  Angle     :  0.535   5.940   6684  Z= 0.310
  Chirality :  0.039   0.135    704
  Planarity :  0.003   0.025    888
  Dihedral  :  3.874  21.979    668
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  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:  3.17 (0.36), residues: 580
  helix:  2.84 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.21 (0.57), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 211 
 PHE   0.006   0.001   PHE B 350 
 TYR   0.008   0.001   TYR C 314 
 ARG   0.007   0.000   ARG C 299 

********************** 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
  191 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.744 
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: 0.8563 (m100) cc_final: 0.7570 (m100)
REVERT: A  221 TRP cc_start: 0.8519 (t-100) cc_final: 0.8153 (t-100)
REVERT: A  222 ARG cc_start: 0.8923 (mtt-85) cc_final: 0.8569 (mtt-85)
REVERT: A  227 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8602 (mm-30)
REVERT: A  242 VAL cc_start: 0.9292 (p) cc_final: 0.8998 (p)
REVERT: A  252 ASN cc_start: 0.8849 (m-40) cc_final: 0.8648 (m-40)
REVERT: A  255 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8411 (mtm-85)
REVERT: A  270 MET cc_start: 0.7791 (mtp) cc_final: 0.7447 (mtp)
REVERT: A  272 MET cc_start: 0.7891 (mmm) cc_final: 0.7439 (mmm)
REVERT: A  275 PHE cc_start: 0.8595 (m-80) cc_final: 0.8234 (m-80)
REVERT: A  299 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7828 (ttm170)
REVERT: A  309 GLU cc_start: 0.9056 (pm20) cc_final: 0.8835 (pm20)
REVERT: A  310 ASN cc_start: 0.8701 (m-40) cc_final: 0.8265 (m110)
REVERT: A  313 ARG cc_start: 0.8949 (mtp180) cc_final: 0.8514 (mtm-85)
REVERT: A  316 LYS cc_start: 0.8377 (tppp) cc_final: 0.7980 (tppp)
REVERT: A  332 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8249 (tpt170)
REVERT: A  344 TYR cc_start: 0.8346 (t80) cc_final: 0.7939 (t80)
REVERT: B  211 TRP cc_start: 0.8866 (m100) cc_final: 0.8032 (m100)
REVERT: B  222 ARG cc_start: 0.9001 (mtt-85) cc_final: 0.8693 (mtt-85)
REVERT: B  246 MET cc_start: 0.9082 (mtp) cc_final: 0.8719 (mtp)
REVERT: B  267 ASN cc_start: 0.8021 (t0) cc_final: 0.7332 (t0)
REVERT: B  275 PHE cc_start: 0.8633 (m-80) cc_final: 0.8211 (m-80)
REVERT: B  282 VAL cc_start: 0.8355 (t) cc_final: 0.8001 (p)
REVERT: B  299 ARG cc_start: 0.8126 (ttm170) cc_final: 0.7734 (ttm170)
REVERT: B  313 ARG cc_start: 0.8725 (mmp80) cc_final: 0.8403 (mtm-85)
REVERT: B  316 LYS cc_start: 0.8060 (mmtp) cc_final: 0.7577 (mmtp)
REVERT: B  322 TYR cc_start: 0.6862 (p90) cc_final: 0.6560 (p90)
REVERT: B  331 LYS cc_start: 0.8926 (mttt) cc_final: 0.7994 (ttmt)
REVERT: B  344 TYR cc_start: 0.8442 (t80) cc_final: 0.8134 (t80)
REVERT: B  352 PRO cc_start: 0.8814 (Cg_exo) cc_final: 0.8597 (Cg_endo)
REVERT: C  217 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8258 (mt-10)
REVERT: C  218 ASP cc_start: 0.8557 (m-30) cc_final: 0.7555 (m-30)
REVERT: C  222 ARG cc_start: 0.9117 (mtt-85) cc_final: 0.8317 (mtt-85)
REVERT: C  244 ARG cc_start: 0.8736 (ttm110) cc_final: 0.8342 (ttm110)
REVERT: C  246 MET cc_start: 0.8928 (mtp) cc_final: 0.8554 (mtp)
REVERT: C  249 ASP cc_start: 0.8801 (t70) cc_final: 0.8446 (t70)
REVERT: C  257 VAL cc_start: 0.8877 (t) cc_final: 0.8624 (t)
REVERT: C  262 MET cc_start: 0.7964 (tmm) cc_final: 0.7250 (tmm)
REVERT: C  275 PHE cc_start: 0.8775 (m-80) cc_final: 0.8262 (m-80)
REVERT: C  282 VAL cc_start: 0.8279 (t) cc_final: 0.6858 (t)
REVERT: C  299 ARG cc_start: 0.8536 (ptt90) cc_final: 0.8268 (ttp-110)
REVERT: C  302 ASP cc_start: 0.9027 (t0) cc_final: 0.8706 (t0)
REVERT: C  304 ASP cc_start: 0.7144 (t0) cc_final: 0.6429 (t0)
REVERT: C  316 LYS cc_start: 0.8369 (tppp) cc_final: 0.7970 (tppp)
REVERT: C  322 TYR cc_start: 0.6912 (p90) cc_final: 0.6531 (p90)
REVERT: C  344 TYR cc_start: 0.8498 (t80) cc_final: 0.8136 (t80)
REVERT: C  348 TYR cc_start: 0.7809 (t80) cc_final: 0.7419 (t80)
REVERT: D  221 TRP cc_start: 0.8526 (t-100) cc_final: 0.8247 (t-100)
REVERT: D  242 VAL cc_start: 0.9036 (t) cc_final: 0.8751 (t)
REVERT: D  245 ASP cc_start: 0.8907 (m-30) cc_final: 0.8676 (m-30)
REVERT: D  246 MET cc_start: 0.8678 (ptp) cc_final: 0.8474 (ptp)
REVERT: D  309 GLU cc_start: 0.8904 (pm20) cc_final: 0.8639 (pp20)
REVERT: D  316 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7485 (mmmm)
REVERT: D  344 TYR cc_start: 0.8576 (t80) cc_final: 0.8134 (t80)
REVERT: D  348 TYR cc_start: 0.7868 (t80) cc_final: 0.7488 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.3254
  time to fit residues: 72.3535
Evaluate side-chains
  190 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 0 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.7378

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.096711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.081478 restraints weight = 13161.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.085090 restraints weight = 6771.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.087434 restraints weight = 4133.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.8236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4964  Z= 0.160
  Angle     :  0.552   7.278   6684  Z= 0.316
  Chirality :  0.041   0.135    704
  Planarity :  0.004   0.026    888
  Dihedral  :  3.889  21.852    668
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  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:  3.19 (0.36), residues: 580
  helix:  2.85 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.23 (0.57), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 211 
 PHE   0.006   0.001   PHE C 350 
 TYR   0.007   0.001   TYR C 314 
 ARG   0.006   0.000   ARG B 228 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2377.24 seconds
wall clock time: 43 minutes 49.10 seconds (2629.10 seconds total)