Starting phenix.real_space_refine
on Thu Jul 31 10:43:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p13_13154/07_2025/7p13_13154.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p13_13154/07_2025/7p13_13154.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p13_13154/07_2025/7p13_13154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p13_13154/07_2025/7p13_13154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p13_13154/07_2025/7p13_13154.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p13_13154/07_2025/7p13_13154.cif"
  }
  resolution = 2.29
  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=   0.268 sd=   0.983
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    8463      2.51       5
     N    2408      2.21       5
     O    2653      1.98       5
     H     154      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13727
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 1961
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 17, 'TRANS': 231}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 5.33, per 1000 atoms: 0.39
  Number of scatterers: 13727
  At special positions: 0
  Unit cell: (115.092, 113.424, 102.582, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     O    2653      8.00
     N    2408      7.00
     C    8463      6.00
     H     154      1.00
    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: 3.49
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3346

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 0 sheets defined
      71.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 22
      removed outlier: 3.636A  pdb=" N   GLU A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 79
    Processing helix  chain 'A' and resid 80 through 82
      No H-bonds generated for 'chain 'A' and resid 80 through 82'
    Processing helix  chain 'A' and resid 130 through 142
    Processing helix  chain 'A' and resid 146 through 166
    Processing helix  chain 'A' and resid 167 through 171
    Processing helix  chain 'A' and resid 179 through 223
    Processing helix  chain 'A' and resid 225 through 235
    Processing helix  chain 'A' and resid 242 through 268
      Proline residue:  A 248  - end of helix
    Processing helix  chain 'B' and resid 10 through 22
      removed outlier: 3.636A  pdb=" N   GLU B  22 " --> pdb=" O   ALA B  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 79
    Processing helix  chain 'B' and resid 80 through 82
      No H-bonds generated for 'chain 'B' and resid 80 through 82'
    Processing helix  chain 'B' and resid 130 through 142
    Processing helix  chain 'B' and resid 146 through 166
    Processing helix  chain 'B' and resid 167 through 171
    Processing helix  chain 'B' and resid 179 through 223
    Processing helix  chain 'B' and resid 225 through 235
    Processing helix  chain 'B' and resid 242 through 268
      Proline residue:  B 248  - end of helix
    Processing helix  chain 'C' and resid 10 through 22
      removed outlier: 3.636A  pdb=" N   GLU C  22 " --> pdb=" O   ALA C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 79
    Processing helix  chain 'C' and resid 80 through 82
      No H-bonds generated for 'chain 'C' and resid 80 through 82'
    Processing helix  chain 'C' and resid 130 through 142
    Processing helix  chain 'C' and resid 146 through 166
    Processing helix  chain 'C' and resid 167 through 171
    Processing helix  chain 'C' and resid 179 through 223
    Processing helix  chain 'C' and resid 225 through 235
    Processing helix  chain 'C' and resid 242 through 268
      Proline residue:  C 248  - end of helix
    Processing helix  chain 'D' and resid 10 through 22
      removed outlier: 3.636A  pdb=" N   GLU D  22 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 79
    Processing helix  chain 'D' and resid 80 through 82
      No H-bonds generated for 'chain 'D' and resid 80 through 82'
    Processing helix  chain 'D' and resid 130 through 142
    Processing helix  chain 'D' and resid 146 through 166
    Processing helix  chain 'D' and resid 167 through 171
    Processing helix  chain 'D' and resid 179 through 223
    Processing helix  chain 'D' and resid 225 through 235
    Processing helix  chain 'D' and resid 242 through 268
      Proline residue:  D 248  - end of helix
    Processing helix  chain 'E' and resid 10 through 22
      removed outlier: 3.636A  pdb=" N   GLU E  22 " --> pdb=" O   ALA E  18 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 79
    Processing helix  chain 'E' and resid 80 through 82
      No H-bonds generated for 'chain 'E' and resid 80 through 82'
    Processing helix  chain 'E' and resid 130 through 142
    Processing helix  chain 'E' and resid 146 through 166
    Processing helix  chain 'E' and resid 167 through 171
    Processing helix  chain 'E' and resid 179 through 223
    Processing helix  chain 'E' and resid 225 through 235
    Processing helix  chain 'E' and resid 242 through 268
      Proline residue:  E 248  - end of helix
    Processing helix  chain 'F' and resid 10 through 22
      removed outlier: 3.636A  pdb=" N   GLU F  22 " --> pdb=" O   ALA F  18 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 39 through 79
    Processing helix  chain 'F' and resid 80 through 82
      No H-bonds generated for 'chain 'F' and resid 80 through 82'
    Processing helix  chain 'F' and resid 130 through 142
    Processing helix  chain 'F' and resid 146 through 166
    Processing helix  chain 'F' and resid 167 through 171
    Processing helix  chain 'F' and resid 179 through 223
    Processing helix  chain 'F' and resid 225 through 235
    Processing helix  chain 'F' and resid 242 through 268
      Proline residue:  F 248  - end of helix
    Processing helix  chain 'G' and resid 10 through 22
      removed outlier: 3.636A  pdb=" N   GLU G  22 " --> pdb=" O   ALA G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 39 through 79
    Processing helix  chain 'G' and resid 80 through 82
      No H-bonds generated for 'chain 'G' and resid 80 through 82'
    Processing helix  chain 'G' and resid 130 through 142
    Processing helix  chain 'G' and resid 146 through 166
    Processing helix  chain 'G' and resid 167 through 171
    Processing helix  chain 'G' and resid 179 through 223
    Processing helix  chain 'G' and resid 225 through 235
    Processing helix  chain 'G' and resid 242 through 268
      Proline residue:  G 248  - end of helix

    987 hydrogen bonds defined for protein.
    2919 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: 3.58

  Time building geometry restraints manager: 3.96 seconds

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

  Histogram of bond lengths:
        0.83 -     1.02: 154
        1.02 -     1.21: 49
        1.21 -     1.41: 5677
        1.41 -     1.60: 8043
        1.60 -     1.80: 84
  Bond restraints: 14007
  Sorted by residual:
  bond pdb=" C   LEU G 270 "
       pdb=" N   GLU G 271 "
    ideal  model  delta    sigma   weight residual
    1.329  1.272  0.056 1.60e-02 3.91e+03 1.24e+01
  bond pdb=" C   LEU E 270 "
       pdb=" N   GLU E 271 "
    ideal  model  delta    sigma   weight residual
    1.329  1.273  0.056 1.60e-02 3.91e+03 1.23e+01
  bond pdb=" C   LEU F 270 "
       pdb=" N   GLU F 271 "
    ideal  model  delta    sigma   weight residual
    1.329  1.273  0.056 1.60e-02 3.91e+03 1.22e+01
  bond pdb=" C   LEU C 270 "
       pdb=" N   GLU C 271 "
    ideal  model  delta    sigma   weight residual
    1.329  1.273  0.056 1.60e-02 3.91e+03 1.21e+01
  bond pdb=" C   LEU B 270 "
       pdb=" N   GLU B 271 "
    ideal  model  delta    sigma   weight residual
    1.329  1.273  0.056 1.60e-02 3.91e+03 1.21e+01
  ... (remaining 14002 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 18243
        2.26 -     4.53: 818
        4.53 -     6.79: 112
        6.79 -     9.05: 14
        9.05 -    11.31: 14
  Bond angle restraints: 19201
  Sorted by residual:
  angle pdb=" C   GLU D 258 "
        pdb=" N   LYS D 259 "
        pdb=" CA  LYS D 259 "
      ideal   model   delta    sigma   weight residual
     121.14  115.49    5.65 1.75e+00 3.27e-01 1.04e+01
  angle pdb=" C   GLU E 258 "
        pdb=" N   LYS E 259 "
        pdb=" CA  LYS E 259 "
      ideal   model   delta    sigma   weight residual
     121.14  115.50    5.64 1.75e+00 3.27e-01 1.04e+01
  angle pdb=" C   GLU B 258 "
        pdb=" N   LYS B 259 "
        pdb=" CA  LYS B 259 "
      ideal   model   delta    sigma   weight residual
     121.14  115.54    5.60 1.75e+00 3.27e-01 1.02e+01
  angle pdb=" C   GLU A 258 "
        pdb=" N   LYS A 259 "
        pdb=" CA  LYS A 259 "
      ideal   model   delta    sigma   weight residual
     121.14  115.55    5.59 1.75e+00 3.27e-01 1.02e+01
  angle pdb=" C   GLU G 258 "
        pdb=" N   LYS G 259 "
        pdb=" CA  LYS G 259 "
      ideal   model   delta    sigma   weight residual
     121.14  115.56    5.58 1.75e+00 3.27e-01 1.02e+01
  ... (remaining 19196 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.99: 7475
       14.99 -    29.99: 881
       29.99 -    44.98: 156
       44.98 -    59.97: 21
       59.97 -    74.97: 42
  Dihedral angle restraints: 8575
    sinusoidal: 3444
      harmonic: 5131
  Sorted by residual:
  dihedral pdb=" CA  PRO C 286 "
           pdb=" C   PRO C 286 "
           pdb=" N   PRO C 287 "
           pdb=" CA  PRO C 287 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.65  -31.35     0      5.00e+00 4.00e-02 3.93e+01
  dihedral pdb=" CA  PRO E 286 "
           pdb=" C   PRO E 286 "
           pdb=" N   PRO E 287 "
           pdb=" CA  PRO E 287 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.70  -31.30     0      5.00e+00 4.00e-02 3.92e+01
  dihedral pdb=" CA  PRO D 286 "
           pdb=" C   PRO D 286 "
           pdb=" N   PRO D 287 "
           pdb=" CA  PRO D 287 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.71  -31.29     0      5.00e+00 4.00e-02 3.92e+01
  ... (remaining 8572 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1238
       0.055 -    0.110: 624
       0.110 -    0.165: 161
       0.165 -    0.221: 21
       0.221 -    0.276: 7
  Chirality restraints: 2051
  Sorted by residual:
  chirality pdb=" CA  GLU A 222 "
            pdb=" N   GLU A 222 "
            pdb=" C   GLU A 222 "
            pdb=" CB  GLU A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  GLU E 222 "
            pdb=" N   GLU E 222 "
            pdb=" C   GLU E 222 "
            pdb=" CB  GLU E 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  GLU F 222 "
            pdb=" N   GLU F 222 "
            pdb=" C   GLU F 222 "
            pdb=" CB  GLU F 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.89e+00
  ... (remaining 2048 not shown)

  Planarity restraints: 2562
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 286 "    0.050 5.00e-02 4.00e+02   7.49e-02 8.98e+00
        pdb=" N   PRO D 287 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO D 287 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO D 287 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO E 286 "    0.050 5.00e-02 4.00e+02   7.47e-02 8.93e+00
        pdb=" N   PRO E 287 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO E 287 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO E 287 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 286 "    0.050 5.00e-02 4.00e+02   7.46e-02 8.91e+00
        pdb=" N   PRO A 287 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 287 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 287 "    0.037 5.00e-02 4.00e+02
  ... (remaining 2559 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.60: 422
        2.60 -     3.10: 10723
        3.10 -     3.60: 17626
        3.60 -     4.10: 22963
        4.10 -     4.60: 36459
  Nonbonded interactions: 88193
  Sorted by model distance:
  nonbonded pdb=" HB  THR D 262 "
            pdb=" HG1 THR D 262 "
     model   vdw
     2.103 1.816
  nonbonded pdb=" HB  THR E 262 "
            pdb=" HG1 THR E 262 "
     model   vdw
     2.105 1.816
  nonbonded pdb=" HB  THR C 262 "
            pdb=" HG1 THR C 262 "
     model   vdw
     2.105 1.816
  nonbonded pdb=" HB  THR B 262 "
            pdb=" HG1 THR B 262 "
     model   vdw
     2.119 1.816
  nonbonded pdb=" HB2 GLU F 258 "
            pdb=" HG3 GLU F 258 "
     model   vdw
     2.133 1.952
  ... (remaining 88188 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:             0.400
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     29.080
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  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:12.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
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      :  0.016   0.075  13853  Z= 0.724
  Angle     :  1.063  11.313  18851  Z= 0.565
  Chirality :  0.067   0.276   2051
  Planarity :  0.008   0.075   2555
  Dihedral  : 14.069  74.966   5194
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    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:  2.06 (0.20), residues: 1715
  helix:  1.67 (0.14), residues: 1204
  sheet:  None (None), residues: 0
  loop :  0.86 (0.30), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP C 156 
 HIS   0.008   0.004   HIS D 216 
 PHE   0.051   0.006   PHE F 130 
 TYR   0.029   0.006   TYR G 264 
 ARG   0.017   0.002   ARG E 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15423 (  987)
  hydrogen bonds       : angle       6.04757 ( 2919)
  covalent geometry    : bond        0.01588 (13853)
  covalent geometry    : angle       1.06268 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 373
  time to evaluate  : 1.523 
Fit side-chains
REVERT: B  221 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7619 (ttm170)
REVERT: C   25 MET cc_start: 0.8513 (mtm) cc_final: 0.8097 (mtp)
REVERT: C  130 PHE cc_start: 0.8261 (m-80) cc_final: 0.8049 (m-80)
REVERT: D  245 GLN cc_start: 0.7345 (mm110) cc_final: 0.7037 (tp40)
REVERT: F   11 GLN cc_start: 0.7993 (tt0) cc_final: 0.7760 (pm20)
REVERT: G  205 MET cc_start: 0.8410 (ttp) cc_final: 0.8171 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 373
  average time/residue: 1.8370
  time to fit residues: 729.0989
Evaluate side-chains
  251 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    1.9990
   chunk 127 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 68 optimal weight:    7.9990
   chunk 131 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 80 optimal weight:    0.4980
   chunk 98 optimal weight:    9.9990
   chunk 152 optimal weight:    0.0010
   overall best weight:    0.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  55 ASN
A 245 GLN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
C  11 GLN
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 239 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  55 ASN
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 245 GLN
E 254 GLN
** F  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 245 GLN
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  55 ASN
G 245 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.091986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.082946 restraints weight = 22273.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.12
r_work: 0.3067 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 2.56 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13853  Z= 0.107
  Angle     :  0.489   7.517  18851  Z= 0.255
  Chirality :  0.034   0.124   2051
  Planarity :  0.005   0.062   2555
  Dihedral  :  3.935  14.495   1883
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 10.89 %
    Favored  : 87.30 %
  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:  4.34 (0.20), residues: 1715
  helix:  3.68 (0.14), residues: 1190
  sheet:  None (None), residues: 0
  loop :  0.92 (0.31), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 156 
 HIS   0.003   0.001   HIS A 216 
 PHE   0.013   0.002   PHE C 152 
 TYR   0.016   0.002   TYR C 264 
 ARG   0.004   0.001   ARG G 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04212 (  987)
  hydrogen bonds       : angle       3.86368 ( 2919)
  covalent geometry    : bond        0.00218 (13853)
  covalent geometry    : angle       0.48875 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 319
  time to evaluate  : 1.493 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8703 (ttpp)
REVERT: C   25 MET cc_start: 0.8801 (mtm) cc_final: 0.8464 (mtp)
REVERT: D  134 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8699 (ttpp)
REVERT: E   81 TYR cc_start: 0.8176 (m-80) cc_final: 0.7971 (m-80)
REVERT: F   11 GLN cc_start: 0.7985 (tt0) cc_final: 0.7705 (pm20)
REVERT: F  233 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7647 (tt0)
REVERT: G  205 MET cc_start: 0.8875 (ttp) cc_final: 0.8633 (ttp)
  outliers start: 25
  outliers final: 10
  residues processed: 335
  average time/residue: 1.4133
  time to fit residues: 511.5370
Evaluate side-chains
  288 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 275
  time to evaluate  : 1.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue   65 LYS
Chi-restraints excluded: chain B residue  134 LYS
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain C residue  233 GLU
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain D residue  134 LYS
Chi-restraints excluded: chain E residue  244 ASP
Chi-restraints excluded: chain F residue  233 GLU
Chi-restraints excluded: chain G residue  202 SER
Chi-restraints excluded: chain G residue  233 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 140 optimal weight:    0.2980
   chunk 70 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 127 optimal weight:    0.2980
   chunk 99 optimal weight:    5.9990
   chunk 136 optimal weight:    6.9990
   chunk 156 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 133 optimal weight:   10.0000
   chunk 104 optimal weight:    0.0030
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN
B  11 GLN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 GLN
C 265 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  55 ASN
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
E 265 ASN
** F  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.092969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.083930 restraints weight = 22310.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.12
r_work: 0.3086 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  13853  Z= 0.089
  Angle     :  0.425   5.942  18851  Z= 0.215
  Chirality :  0.033   0.133   2051
  Planarity :  0.004   0.049   2555
  Dihedral  :  3.436  11.969   1883
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.77 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.88 (0.21), residues: 1715
  helix:  4.04 (0.14), residues: 1232
  sheet:  None (None), residues: 0
  loop :  0.98 (0.32), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 156 
 HIS   0.003   0.001   HIS A 216 
 PHE   0.014   0.002   PHE B 152 
 TYR   0.011   0.001   TYR G 236 
 ARG   0.004   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03556 (  987)
  hydrogen bonds       : angle       3.55151 ( 2919)
  covalent geometry    : bond        0.00176 (13853)
  covalent geometry    : angle       0.42467 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 298
  time to evaluate  : 1.753 
Fit side-chains
   revert: symmetry clash
REVERT: B  134 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8733 (ttpp)
REVERT: C   25 MET cc_start: 0.8788 (mtm) cc_final: 0.8440 (mtp)
REVERT: F   11 GLN cc_start: 0.8018 (tt0) cc_final: 0.7729 (pm20)
REVERT: F  233 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7601 (tt0)
REVERT: G  134 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8718 (ttpp)
REVERT: G  205 MET cc_start: 0.8872 (ttp) cc_final: 0.8607 (ttp)
  outliers start: 29
  outliers final: 12
  residues processed: 315
  average time/residue: 1.7993
  time to fit residues: 610.0510
Evaluate side-chains
  297 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 282
  time to evaluate  : 1.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LYS
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue  134 LYS
Chi-restraints excluded: chain C residue  233 GLU
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain E residue    8 THR
Chi-restraints excluded: chain E residue  244 ASP
Chi-restraints excluded: chain F residue  134 LYS
Chi-restraints excluded: chain F residue  233 GLU
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain G residue  134 LYS
Chi-restraints excluded: chain G residue  202 SER
Chi-restraints excluded: chain G residue  233 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 129 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 47 optimal weight:    5.9990
   chunk 112 optimal weight:    8.9990
   chunk 116 optimal weight:    5.9990
   chunk 140 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 137 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0040
   overall best weight:    1.1596

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  68 GLN
A 265 ASN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 GLN
C 265 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
E 265 ASN
** F  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.092697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.083643 restraints weight = 22162.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 1.11
r_work: 0.3078 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  13853  Z= 0.102
  Angle     :  0.417   4.688  18851  Z= 0.214
  Chirality :  0.033   0.120   2051
  Planarity :  0.004   0.040   2555
  Dihedral  :  3.309  11.011   1883
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 12.84 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.14 (0.21), residues: 1715
  helix:  4.24 (0.14), residues: 1218
  sheet:  None (None), residues: 0
  loop :  1.14 (0.31), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 156 
 HIS   0.004   0.001   HIS B 216 
 PHE   0.016   0.002   PHE B 152 
 TYR   0.012   0.001   TYR D 236 
 ARG   0.004   0.000   ARG F 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03610 (  987)
  hydrogen bonds       : angle       3.47330 ( 2919)
  covalent geometry    : bond        0.00212 (13853)
  covalent geometry    : angle       0.41667 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 288
  time to evaluate  : 2.004 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8693 (ttpp)
REVERT: B  134 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8726 (ttpp)
REVERT: C   25 MET cc_start: 0.8756 (mtm) cc_final: 0.8446 (mtp)
REVERT: F   11 GLN cc_start: 0.8034 (tt0) cc_final: 0.7736 (pm20)
REVERT: F  233 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7587 (tt0)
REVERT: G  134 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8736 (ttpp)
REVERT: G  205 MET cc_start: 0.8862 (ttp) cc_final: 0.8599 (ttp)
  outliers start: 37
  outliers final: 15
  residues processed: 310
  average time/residue: 1.5430
  time to fit residues: 516.2157
Evaluate side-chains
  297 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 278
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LYS
Chi-restraints excluded: chain A residue  168 LYS
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  134 LYS
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain C residue  233 GLU
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain F residue  131 MET
Chi-restraints excluded: chain F residue  134 LYS
Chi-restraints excluded: chain F residue  233 GLU
Chi-restraints excluded: chain F residue  246 ILE
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain G residue  134 LYS
Chi-restraints excluded: chain G residue  202 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 137 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 149 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 146 optimal weight:    0.0870
   chunk 159 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 134 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
B 254 GLN
** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 GLN
C 265 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
E 265 ASN
** F  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.093758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.084711 restraints weight = 22361.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.12
r_work: 0.3098 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018  13853  Z= 0.079
  Angle     :  0.390   4.994  18851  Z= 0.197
  Chirality :  0.032   0.121   2051
  Planarity :  0.003   0.033   2555
  Dihedral  :  3.142  10.579   1883
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.07 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.31 (0.21), residues: 1715
  helix:  4.34 (0.14), residues: 1225
  sheet:  None (None), residues: 0
  loop :  1.23 (0.32), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 156 
 HIS   0.003   0.001   HIS B 216 
 PHE   0.014   0.001   PHE B 152 
 TYR   0.012   0.001   TYR D 236 
 ARG   0.004   0.000   ARG B 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03224 (  987)
  hydrogen bonds       : angle       3.33295 ( 2919)
  covalent geometry    : bond        0.00155 (13853)
  covalent geometry    : angle       0.38953 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 295
  time to evaluate  : 1.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8629 (ttpp)
REVERT: A  221 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7915 (ttm110)
REVERT: C   25 MET cc_start: 0.8731 (mtm) cc_final: 0.8413 (mtp)
REVERT: C  245 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6905 (mp10)
REVERT: F   11 GLN cc_start: 0.7994 (tt0) cc_final: 0.7701 (pm20)
REVERT: G  205 MET cc_start: 0.8844 (ttp) cc_final: 0.8592 (ttp)
  outliers start: 27
  outliers final: 7
  residues processed: 307
  average time/residue: 1.4638
  time to fit residues: 483.3871
Evaluate side-chains
  290 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 280
  time to evaluate  : 1.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LYS
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  221 ARG
Chi-restraints excluded: chain C residue  233 GLU
Chi-restraints excluded: chain C residue  245 GLN
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain F residue  202 SER
Chi-restraints excluded: chain G residue   65 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 150 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 157 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 126 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 GLN
C 265 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
E 265 ASN
** F  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.093309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.084197 restraints weight = 22399.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.12
r_work: 0.3088 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  13853  Z= 0.094
  Angle     :  0.403   4.624  18851  Z= 0.206
  Chirality :  0.032   0.120   2051
  Planarity :  0.004   0.042   2555
  Dihedral  :  3.122  10.545   1883
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.72 %
    Favored  : 83.04 %
  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:  5.33 (0.21), residues: 1715
  helix:  4.33 (0.14), residues: 1225
  sheet:  None (None), residues: 0
  loop :  1.31 (0.32), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 156 
 HIS   0.004   0.001   HIS B 216 
 PHE   0.016   0.002   PHE B 152 
 TYR   0.018   0.001   TYR F 236 
 ARG   0.003   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03421 (  987)
  hydrogen bonds       : angle       3.34327 ( 2919)
  covalent geometry    : bond        0.00194 (13853)
  covalent geometry    : angle       0.40350 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 283
  time to evaluate  : 2.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8659 (ttpp)
REVERT: A  221 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7923 (ttm110)
REVERT: C   25 MET cc_start: 0.8738 (mtm) cc_final: 0.8409 (mtp)
REVERT: F   11 GLN cc_start: 0.8041 (tt0) cc_final: 0.7727 (pm20)
REVERT: F  233 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7594 (tt0)
REVERT: G  205 MET cc_start: 0.8858 (ttp) cc_final: 0.8613 (ttp)
  outliers start: 31
  outliers final: 15
  residues processed: 297
  average time/residue: 1.5315
  time to fit residues: 490.0206
Evaluate side-chains
  297 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 279
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue  134 LYS
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  221 ARG
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain C residue  233 GLU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain F residue  131 MET
Chi-restraints excluded: chain F residue  202 SER
Chi-restraints excluded: chain F residue  233 GLU
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain G residue  202 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 130 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   chunk 126 optimal weight:    0.9980
   chunk 150 optimal weight:    0.9990
   chunk 155 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 106 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 120 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 GLN
C 265 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
E 265 ASN
F  48 GLN
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.091704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.082689 restraints weight = 22365.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.11
r_work: 0.3060 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  13853  Z= 0.143
  Angle     :  0.452   4.903  18851  Z= 0.234
  Chirality :  0.034   0.120   2051
  Planarity :  0.004   0.046   2555
  Dihedral  :  3.273  10.330   1883
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.22 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.11 (0.21), residues: 1715
  helix:  4.17 (0.14), residues: 1218
  sheet:  None (None), residues: 0
  loop :  1.26 (0.31), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 156 
 HIS   0.006   0.002   HIS B 216 
 PHE   0.020   0.002   PHE B 152 
 TYR   0.021   0.002   TYR F 236 
 ARG   0.003   0.000   ARG E 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04023 (  987)
  hydrogen bonds       : angle       3.52368 ( 2919)
  covalent geometry    : bond        0.00307 (13853)
  covalent geometry    : angle       0.45166 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 270
  time to evaluate  : 1.626 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8704 (ttpp)
REVERT: C   25 MET cc_start: 0.8760 (mtm) cc_final: 0.8405 (mtp)
REVERT: F   11 GLN cc_start: 0.8069 (tt0) cc_final: 0.7755 (pm20)
REVERT: F  233 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7571 (tt0)
REVERT: G  134 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8691 (ttpp)
REVERT: G  205 MET cc_start: 0.8866 (ttp) cc_final: 0.8615 (ttp)
  outliers start: 33
  outliers final: 15
  residues processed: 286
  average time/residue: 1.5950
  time to fit residues: 489.4352
Evaluate side-chains
  291 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 273
  time to evaluate  : 1.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue  134 LYS
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain C residue  233 GLU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue  202 SER
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain F residue  233 GLU
Chi-restraints excluded: chain F residue  246 ILE
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain G residue  134 LYS
Chi-restraints excluded: chain G residue  202 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 162 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 48 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 139 optimal weight:    5.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 265 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
F 254 GLN
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.092734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.083657 restraints weight = 22289.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.11
r_work: 0.3077 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  13853  Z= 0.102
  Angle     :  0.413   4.981  18851  Z= 0.213
  Chirality :  0.033   0.122   2051
  Planarity :  0.004   0.040   2555
  Dihedral  :  3.185  10.344   1883
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.80 %
    Favored  : 82.11 %
  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:  5.22 (0.21), residues: 1715
  helix:  4.26 (0.14), residues: 1218
  sheet:  None (None), residues: 0
  loop :  1.29 (0.31), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 156 
 HIS   0.004   0.001   HIS B 216 
 PHE   0.016   0.002   PHE C 152 
 TYR   0.018   0.001   TYR F 236 
 ARG   0.004   0.000   ARG B 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03626 (  987)
  hydrogen bonds       : angle       3.43626 ( 2919)
  covalent geometry    : bond        0.00211 (13853)
  covalent geometry    : angle       0.41282 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 279
  time to evaluate  : 1.684 
Fit side-chains
REVERT: A  134 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8668 (ttpp)
REVERT: C   25 MET cc_start: 0.8754 (mtm) cc_final: 0.8414 (mtp)
REVERT: F   11 GLN cc_start: 0.8059 (tt0) cc_final: 0.7736 (pm20)
REVERT: F  233 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7600 (tt0)
REVERT: G  134 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8688 (ttpp)
REVERT: G  205 MET cc_start: 0.8849 (ttp) cc_final: 0.8607 (ttp)
  outliers start: 29
  outliers final: 14
  residues processed: 294
  average time/residue: 1.5732
  time to fit residues: 496.6121
Evaluate side-chains
  292 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 275
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue  134 LYS
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue  233 GLU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue  202 SER
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain F residue  233 GLU
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain G residue  134 LYS
Chi-restraints excluded: chain G residue  202 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 142 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0670
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 145 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 120 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.4124

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 265 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
E 265 ASN
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.092377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.083337 restraints weight = 22221.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.10
r_work: 0.3073 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 2.58 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  13853  Z= 0.113
  Angle     :  0.425   5.100  18851  Z= 0.219
  Chirality :  0.033   0.120   2051
  Planarity :  0.004   0.042   2555
  Dihedral  :  3.186  10.336   1883
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.31 %
    Favored  : 81.89 %
  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:  5.19 (0.21), residues: 1715
  helix:  4.24 (0.14), residues: 1218
  sheet:  None (None), residues: 0
  loop :  1.28 (0.31), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 156 
 HIS   0.005   0.001   HIS B 216 
 PHE   0.017   0.002   PHE C 152 
 TYR   0.019   0.002   TYR G 236 
 ARG   0.004   0.000   ARG G 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03731 (  987)
  hydrogen bonds       : angle       3.45946 ( 2919)
  covalent geometry    : bond        0.00240 (13853)
  covalent geometry    : angle       0.42494 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 274
  time to evaluate  : 1.840 
Fit side-chains
REVERT: A  134 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8699 (ttpp)
REVERT: C   25 MET cc_start: 0.8734 (mtm) cc_final: 0.8397 (mtp)
REVERT: F   11 GLN cc_start: 0.8063 (tt0) cc_final: 0.7738 (pm20)
REVERT: F  233 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7586 (tt0)
REVERT: G  134 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8690 (ttpp)
REVERT: G  205 MET cc_start: 0.8849 (ttp) cc_final: 0.8605 (ttp)
  outliers start: 25
  outliers final: 14
  residues processed: 285
  average time/residue: 2.0561
  time to fit residues: 630.9530
Evaluate side-chains
  294 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 277
  time to evaluate  : 2.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue  134 LYS
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain C residue  233 GLU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain E residue   65 LYS
Chi-restraints excluded: chain E residue  246 ILE
Chi-restraints excluded: chain F residue  233 GLU
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain G residue  134 LYS
Chi-restraints excluded: chain G residue  202 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 120 optimal weight:   10.0000
   chunk 114 optimal weight:    8.9990
   chunk 60 optimal weight:    0.5980
   chunk 141 optimal weight:    4.9990
   chunk 133 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 154 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 160 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 265 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
E 265 ASN
F 254 GLN
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.093502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.084445 restraints weight = 22358.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.11
r_work: 0.3104 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  13853  Z= 0.085
  Angle     :  0.396   4.818  18851  Z= 0.202
  Chirality :  0.032   0.122   2051
  Planarity :  0.003   0.035   2555
  Dihedral  :  3.062  10.558   1883
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.74 %
    Favored  : 81.82 %
  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:  5.41 (0.21), residues: 1715
  helix:  4.42 (0.14), residues: 1218
  sheet:  None (None), residues: 0
  loop :  1.31 (0.31), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 156 
 HIS   0.003   0.001   HIS F 216 
 PHE   0.014   0.001   PHE B 152 
 TYR   0.017   0.001   TYR G 236 
 ARG   0.004   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03316 (  987)
  hydrogen bonds       : angle       3.32024 ( 2919)
  covalent geometry    : bond        0.00172 (13853)
  covalent geometry    : angle       0.39604 (18851)

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

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

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3430 Ramachandran restraints generated.
    1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 289
  time to evaluate  : 2.857 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8654 (ttpp)
REVERT: C   25 MET cc_start: 0.8709 (mtm) cc_final: 0.8352 (mtp)
REVERT: F   11 GLN cc_start: 0.8064 (tt0) cc_final: 0.7700 (pm20)
REVERT: G  134 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8622 (ttpp)
REVERT: G  205 MET cc_start: 0.8824 (ttp) cc_final: 0.8578 (ttp)
  outliers start: 20
  outliers final: 11
  residues processed: 298
  average time/residue: 2.4620
  time to fit residues: 797.7303
Evaluate side-chains
  291 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 278
  time to evaluate  : 2.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue  134 LYS
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain C residue  233 GLU
Chi-restraints excluded: chain D residue    8 THR
Chi-restraints excluded: chain D residue  244 ASP
Chi-restraints excluded: chain F residue  282 ILE
Chi-restraints excluded: chain G residue   65 LYS
Chi-restraints excluded: chain G residue  134 LYS
Chi-restraints excluded: chain G residue  202 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 128 optimal weight:    0.0020
   chunk 39 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 116 optimal weight:    0.4980
   chunk 56 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 115 optimal weight:    7.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.0592

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  68 GLN
A 265 ASN
** B  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 254 GLN
** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 265 ASN
** D  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 254 GLN
F 254 GLN
F 265 ASN
** G  48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.093272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.084154 restraints weight = 22414.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.11
r_work: 0.3098 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016  13853  Z= 0.095
  Angle     :  0.404   4.804  18851  Z= 0.206
  Chirality :  0.033   0.120   2051
  Planarity :  0.003   0.034   2555
  Dihedral  :  3.063  10.613   1883
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 17.10 %
    Favored  : 81.60 %
  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:  5.39 (0.21), residues: 1715
  helix:  4.40 (0.14), residues: 1218
  sheet:  None (None), residues: 0
  loop :  1.32 (0.31), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 156 
 HIS   0.004   0.001   HIS F 216 
 PHE   0.016   0.002   PHE B 152 
 TYR   0.018   0.001   TYR G 236 
 ARG   0.005   0.000   ARG B 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03441 (  987)
  hydrogen bonds       : angle       3.33856 ( 2919)
  covalent geometry    : bond        0.00198 (13853)
  covalent geometry    : angle       0.40426 (18851)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13857.76 seconds
wall clock time: 250 minutes 34.81 seconds (15034.81 seconds total)