Starting phenix.real_space_refine
on Tue Feb  3 18:49:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w1p_65553/02_2026/9w1p_65553.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w1p_65553/02_2026/9w1p_65553.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w1p_65553/02_2026/9w1p_65553.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w1p_65553/02_2026/9w1p_65553.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w1p_65553/02_2026/9w1p_65553.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w1p_65553/02_2026/9w1p_65553.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.000 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      36      5.16       5
     C    4080      2.51       5
     N     976      2.21       5
     O    1110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6204
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 403, 3086
          Classifications: {'peptide': 403}
          Link IDs: {'PTRANS': 15, 'TRANS': 387}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'G6P': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.06, per 1000 atoms: 0.33
  Number of scatterers: 6204
  At special positions: 0
  Unit cell: (88.81, 75.53, 70.55, 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      36     16.00
     P       2     15.00
     O    1110      8.00
     N     976      7.00
     C    4080      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: 0.54
  Conformation dependent library (CDL) restraints added in 409.6 milliseconds
  

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1456

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      92.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 29
      removed outlier: 4.019A  pdb=" N   TYR A   9 " --> pdb=" O   GLY A   5 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS A  29 " --> pdb=" O   TYR A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 42
      Proline residue:  A  36  - end of helix
    Processing helix  chain 'A' and resid 45 through 74
      removed outlier: 4.133A  pdb=" N   PHE A  65 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLN A  73 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 97
    Processing helix  chain 'A' and resid 99 through 129
      removed outlier: 4.306A  pdb=" N   TRP A 118 " --> pdb=" O   GLN A 114 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 133 through 151
      removed outlier: 3.646A  pdb=" N   SER A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   MET A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ASN A 146 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 163
    Processing helix  chain 'A' and resid 164 through 187
      removed outlier: 3.502A  pdb=" N   ILE A 187 " --> pdb=" O   CYS A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'A' and resid 216 through 222
    Processing helix  chain 'A' and resid 223 through 253
      removed outlier: 3.761A  pdb=" N   TRP A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   GLN A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   PHE A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 291
    Processing helix  chain 'A' and resid 300 through 321
      removed outlier: 3.582A  pdb=" N   LEU A 304 " --> pdb=" O   ARG A 300 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   PHE A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 341
    Processing helix  chain 'A' and resid 342 through 356
    Processing helix  chain 'A' and resid 361 through 391
      removed outlier: 3.770A  pdb=" N   LEU A 382 " --> pdb=" O   PHE A 378 " (cutoff:3.500A)
      Proline residue:  A 383  - end of helix
    Processing helix  chain 'A' and resid 392 through 425
    Processing helix  chain 'B' and resid 6 through 29
      removed outlier: 3.508A  pdb=" N   LYS B  29 " --> pdb=" O   TYR B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 42
      Proline residue:  B  36  - end of helix
    Processing helix  chain 'B' and resid 45 through 74
      removed outlier: 4.133A  pdb=" N   PHE B  65 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLN B  73 " --> pdb=" O   VAL B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 97
    Processing helix  chain 'B' and resid 99 through 129
      removed outlier: 4.305A  pdb=" N   TRP B 118 " --> pdb=" O   GLN B 114 " (cutoff:3.500A)
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 133 through 151
      removed outlier: 3.646A  pdb=" N   SER B 144 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   MET B 145 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ASN B 146 " --> pdb=" O   SER B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 163
    Processing helix  chain 'B' and resid 164 through 187
      removed outlier: 3.503A  pdb=" N   ILE B 187 " --> pdb=" O   CYS B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 194
    Processing helix  chain 'B' and resid 216 through 222
    Processing helix  chain 'B' and resid 223 through 253
      removed outlier: 3.761A  pdb=" N   TRP B 227 " --> pdb=" O   SER B 223 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   GLN B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   PHE B 249 " --> pdb=" O   ASP B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 291
    Processing helix  chain 'B' and resid 300 through 321
      removed outlier: 3.583A  pdb=" N   LEU B 304 " --> pdb=" O   ARG B 300 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   PHE B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 341
    Processing helix  chain 'B' and resid 342 through 356
    Processing helix  chain 'B' and resid 361 through 391
      removed outlier: 3.770A  pdb=" N   LEU B 382 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
      Proline residue:  B 383  - end of helix
    Processing helix  chain 'B' and resid 392 through 425

    564 hydrogen bonds defined for protein.
    1680 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: 1.15

  Time building geometry restraints manager: 0.76 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: 1385
        1.33 -     1.45: 1530
        1.45 -     1.57: 3401
        1.57 -     1.69: 2
        1.69 -     1.81: 58
  Bond restraints: 6376
  Sorted by residual:
  bond pdb=" C1  G6P A 601 "
       pdb=" O5  G6P A 601 "
    ideal  model  delta    sigma   weight residual
    1.401  1.509 -0.108 2.00e-02 2.50e+03 2.90e+01
  bond pdb=" C1  G6P B 601 "
       pdb=" O5  G6P B 601 "
    ideal  model  delta    sigma   weight residual
    1.401  1.508 -0.107 2.00e-02 2.50e+03 2.88e+01
  bond pdb=" O6  G6P B 601 "
       pdb=" P   G6P B 601 "
    ideal  model  delta    sigma   weight residual
    1.722  1.663  0.059 2.00e-02 2.50e+03 8.72e+00
  bond pdb=" O6  G6P A 601 "
       pdb=" P   G6P A 601 "
    ideal  model  delta    sigma   weight residual
    1.722  1.664  0.058 2.00e-02 2.50e+03 8.53e+00
  bond pdb=" C5  G6P B 601 "
       pdb=" O5  G6P B 601 "
    ideal  model  delta    sigma   weight residual
    1.419  1.475 -0.056 2.00e-02 2.50e+03 7.71e+00
  ... (remaining 6371 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 8237
        1.93 -     3.86: 348
        3.86 -     5.79: 73
        5.79 -     7.72: 14
        7.72 -     9.66: 6
  Bond angle restraints: 8678
  Sorted by residual:
  angle pdb=" N   TRP A 118 "
        pdb=" CA  TRP A 118 "
        pdb=" C   TRP A 118 "
      ideal   model   delta    sigma   weight residual
     109.81  119.47   -9.66 2.21e+00 2.05e-01 1.91e+01
  angle pdb=" N   TRP B 118 "
        pdb=" CA  TRP B 118 "
        pdb=" C   TRP B 118 "
      ideal   model   delta    sigma   weight residual
     109.81  119.45   -9.64 2.21e+00 2.05e-01 1.90e+01
  angle pdb=" N   PRO A 119 "
        pdb=" CA  PRO A 119 "
        pdb=" C   PRO A 119 "
      ideal   model   delta    sigma   weight residual
     110.70  115.28   -4.58 1.22e+00 6.72e-01 1.41e+01
  angle pdb=" N   PRO B 119 "
        pdb=" CA  PRO B 119 "
        pdb=" C   PRO B 119 "
      ideal   model   delta    sigma   weight residual
     110.70  115.26   -4.56 1.22e+00 6.72e-01 1.40e+01
  angle pdb=" N   LEU A 382 "
        pdb=" CA  LEU A 382 "
        pdb=" C   LEU A 382 "
      ideal   model   delta    sigma   weight residual
     109.81  116.79   -6.98 2.21e+00 2.05e-01 9.97e+00
  ... (remaining 8673 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.08: 3443
       15.08 -    30.15: 152
       30.15 -    45.23: 40
       45.23 -    60.31: 3
       60.31 -    75.38: 6
  Dihedral angle restraints: 3644
    sinusoidal: 1356
      harmonic: 2288
  Sorted by residual:
  dihedral pdb=" CA  SER B  63 "
           pdb=" C   SER B  63 "
           pdb=" N   LYS B  64 "
           pdb=" CA  LYS B  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.62   16.38     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  SER A  63 "
           pdb=" C   SER A  63 "
           pdb=" N   LYS A  64 "
           pdb=" CA  LYS A  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.63   16.37     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  TRP B 137 "
           pdb=" C   TRP B 137 "
           pdb=" N   TRP B 138 "
           pdb=" CA  TRP B 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.82   16.18     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 3641 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 770
       0.059 -    0.118: 179
       0.118 -    0.177: 21
       0.177 -    0.236: 6
       0.236 -    0.295: 6
  Chirality restraints: 982
  Sorted by residual:
  chirality pdb=" C1  G6P B 601 "
            pdb=" C2  G6P B 601 "
            pdb=" O1  G6P B 601 "
            pdb=" O5  G6P B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.03   -2.33    0.29 2.00e-01 2.50e+01 2.17e+00
  chirality pdb=" C1  G6P A 601 "
            pdb=" C2  G6P A 601 "
            pdb=" O1  G6P A 601 "
            pdb=" O5  G6P A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.03   -2.32    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  VAL B  34 "
            pdb=" CA  VAL B  34 "
            pdb=" CG1 VAL B  34 "
            pdb=" CG2 VAL B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 979 not shown)

  Planarity restraints: 1058
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 119 "   -0.038 5.00e-02 4.00e+02   5.65e-02 5.10e+00
        pdb=" N   PRO B 120 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 120 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 120 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 119 "   -0.038 5.00e-02 4.00e+02   5.64e-02 5.09e+00
        pdb=" N   PRO A 120 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 120 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 120 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 344 "    0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO A 345 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 345 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 345 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1055 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 2225
        2.87 -     3.38: 6309
        3.38 -     3.88: 11096
        3.88 -     4.39: 11887
        4.39 -     4.90: 20922
  Nonbonded interactions: 52439
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  72 "
            pdb=" OG1 THR A 364 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" OD2 ASP B  72 "
            pdb=" OG1 THR B 364 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" O   ALA B 139 "
            pdb=" OG1 THR B 143 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" O   ALA A 139 "
            pdb=" OG1 THR A 143 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" O   VAL B  69 "
            pdb=" NE2 GLN B  73 "
     model   vdw
     2.395 3.120
  ... (remaining 52434 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             5.500
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.880
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:1.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
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   0.108   6376  Z= 0.330
  Angle     :  0.957   9.656   8678  Z= 0.502
  Chirality :  0.055   0.295    982
  Planarity :  0.009   0.056   1058
  Dihedral  : 10.021  75.383   2188
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (0.23), residues: 794
  helix: -1.83 (0.14), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.26 (0.62), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  28 
 TYR   0.026   0.003   TYR B 343 
 PHE   0.032   0.004   PHE A  33 
 TRP   0.028   0.003   TRP B 138 
 HIS   0.004   0.002   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00762 ( 6376)
  covalent geometry    : angle       0.95677 ( 8678)
  hydrogen bonds       : bond        0.11376 (  564)
  hydrogen bonds       : angle       6.10744 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A  127 LYS cc_start: 0.8327 (mmtm) cc_final: 0.7918 (mmmt)
REVERT: B   35 MET cc_start: 0.7708 (tpp) cc_final: 0.7392 (tpp)
REVERT: B  340 PHE cc_start: 0.8045 (t80) cc_final: 0.7726 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0933
  time to fit residues: 13.2242
Evaluate side-chains
  80 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
A  91 ASN
A 257 GLN
B  27 ASN
B  91 ASN
B 257 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.137855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.119724 restraints weight = 7055.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.88
r_work: 0.3237 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6376  Z= 0.171
  Angle     :  0.586   7.206   8678  Z= 0.311
  Chirality :  0.038   0.136    982
  Planarity :  0.006   0.049   1058
  Dihedral  :  4.181  13.963    900
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  :  4.94 %
    Favored  : 93.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.27), residues: 794
  helix:  0.47 (0.18), residues: 704
  sheet:  None (None), residues: 0
  loop :  0.54 (0.65), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 126 
 TYR   0.013   0.002   TYR B  25 
 PHE   0.022   0.002   PHE B  33 
 TRP   0.021   0.002   TRP A 138 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6376)
  covalent geometry    : angle       0.58594 ( 8678)
  hydrogen bonds       : bond        0.04512 (  564)
  hydrogen bonds       : angle       4.29139 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   10 ARG cc_start: 0.7775 (mmt90) cc_final: 0.7569 (mmt90)
REVERT: A  127 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7823 (mmmt)
REVERT: A  190 GLU cc_start: 0.7776 (pm20) cc_final: 0.7352 (pt0)
REVERT: A  340 PHE cc_start: 0.8015 (t80) cc_final: 0.7803 (t80)
REVERT: B  127 LYS cc_start: 0.8264 (mmtm) cc_final: 0.7862 (mmmt)
REVERT: B  190 GLU cc_start: 0.7661 (pm20) cc_final: 0.7193 (pt0)
REVERT: B  340 PHE cc_start: 0.8077 (t80) cc_final: 0.7818 (t80)
  outliers start: 11
  outliers final: 6
  residues processed: 86
  average time/residue: 0.0952
  time to fit residues: 10.6423
Evaluate side-chains
  79 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   90 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.129512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.112096 restraints weight = 7387.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.95
r_work: 0.3152 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3008 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6376  Z= 0.198
  Angle     :  0.607   9.450   8678  Z= 0.311
  Chirality :  0.039   0.129    982
  Planarity :  0.005   0.052   1058
  Dihedral  :  4.066  13.131    900
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  :  8.64 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.29), residues: 794
  helix:  1.28 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.58 (0.66), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 126 
 TYR   0.014   0.002   TYR B  25 
 PHE   0.016   0.002   PHE B  33 
 TRP   0.019   0.002   TRP A 138 
 HIS   0.005   0.002   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 6376)
  covalent geometry    : angle       0.60668 ( 8678)
  hydrogen bonds       : bond        0.04526 (  564)
  hydrogen bonds       : angle       4.11179 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  190 GLU cc_start: 0.7773 (pm20) cc_final: 0.7326 (pt0)
REVERT: A  340 PHE cc_start: 0.8160 (t80) cc_final: 0.7829 (t80)
REVERT: B  190 GLU cc_start: 0.7753 (pm20) cc_final: 0.7419 (pt0)
REVERT: B  340 PHE cc_start: 0.8188 (t80) cc_final: 0.7853 (t80)
REVERT: B  379 LEU cc_start: 0.8571 (tt) cc_final: 0.8359 (tp)
  outliers start: 16
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0800
  time to fit residues: 10.4499
Evaluate side-chains
  92 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   15 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.129766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.112516 restraints weight = 7395.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.94
r_work: 0.3160 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6376  Z= 0.170
  Angle     :  0.561   7.140   8678  Z= 0.289
  Chirality :  0.038   0.124    982
  Planarity :  0.005   0.053   1058
  Dihedral  :  3.941  12.925    900
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  :  9.41 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.31 (0.29), residues: 794
  helix:  1.69 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.66 (0.68), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 126 
 TYR   0.013   0.001   TYR B  25 
 PHE   0.013   0.001   PHE B  33 
 TRP   0.014   0.002   TRP B 138 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 6376)
  covalent geometry    : angle       0.56130 ( 8678)
  hydrogen bonds       : bond        0.04363 (  564)
  hydrogen bonds       : angle       3.94412 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A   96 TRP cc_start: 0.6775 (m100) cc_final: 0.6376 (m100)
REVERT: A  190 GLU cc_start: 0.7783 (pm20) cc_final: 0.7445 (pt0)
REVERT: A  340 PHE cc_start: 0.8156 (t80) cc_final: 0.7802 (t80)
REVERT: B  190 GLU cc_start: 0.7771 (pm20) cc_final: 0.7440 (pt0)
REVERT: B  288 MET cc_start: 0.8436 (tpp) cc_final: 0.8040 (mtp)
REVERT: B  340 PHE cc_start: 0.8189 (t80) cc_final: 0.7865 (t80)
  outliers start: 17
  outliers final: 14
  residues processed: 85
  average time/residue: 0.0796
  time to fit residues: 9.2365
Evaluate side-chains
  85 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   15 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.126867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.109180 restraints weight = 7586.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.99
r_work: 0.3115 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6376  Z= 0.200
  Angle     :  0.587   6.946   8678  Z= 0.302
  Chirality :  0.039   0.129    982
  Planarity :  0.005   0.054   1058
  Dihedral  :  3.985  13.289    900
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  :  8.02 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.29), residues: 794
  helix:  1.77 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.81 (0.69), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 126 
 TYR   0.014   0.002   TYR A  25 
 PHE   0.012   0.002   PHE B  33 
 TRP   0.015   0.002   TRP A 138 
 HIS   0.005   0.002   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 6376)
  covalent geometry    : angle       0.58662 ( 8678)
  hydrogen bonds       : bond        0.04491 (  564)
  hydrogen bonds       : angle       3.99701 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   96 TRP cc_start: 0.6927 (m100) cc_final: 0.6627 (m100)
REVERT: A  190 GLU cc_start: 0.7852 (pm20) cc_final: 0.7522 (pt0)
REVERT: B   96 TRP cc_start: 0.6911 (m100) cc_final: 0.6536 (m100)
REVERT: B  190 GLU cc_start: 0.7841 (pm20) cc_final: 0.7520 (pt0)
  outliers start: 23
  outliers final: 17
  residues processed: 103
  average time/residue: 0.0758
  time to fit residues: 10.6972
Evaluate side-chains
  98 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   15 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 61 optimal weight:    0.6980
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.129454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.111787 restraints weight = 7393.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.96
r_work: 0.3150 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6376  Z= 0.158
  Angle     :  0.543   6.724   8678  Z= 0.281
  Chirality :  0.038   0.120    982
  Planarity :  0.005   0.053   1058
  Dihedral  :  3.907  12.962    900
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  :  8.33 %
    Favored  : 87.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.77 (0.29), residues: 794
  helix:  1.99 (0.19), residues: 702
  sheet:  None (None), residues: 0
  loop :  0.84 (0.68), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 126 
 TYR   0.011   0.001   TYR A  25 
 PHE   0.011   0.001   PHE B 250 
 TRP   0.013   0.001   TRP B 138 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6376)
  covalent geometry    : angle       0.54325 ( 8678)
  hydrogen bonds       : bond        0.04297 (  564)
  hydrogen bonds       : angle       3.86475 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A   96 TRP cc_start: 0.6875 (m100) cc_final: 0.6495 (m100)
REVERT: A  190 GLU cc_start: 0.7854 (pm20) cc_final: 0.7527 (pt0)
REVERT: A  340 PHE cc_start: 0.8222 (t80) cc_final: 0.7812 (t80)
REVERT: B   96 TRP cc_start: 0.6831 (m100) cc_final: 0.6471 (m100)
REVERT: B  190 GLU cc_start: 0.7864 (pm20) cc_final: 0.7533 (pt0)
REVERT: B  340 PHE cc_start: 0.8221 (t80) cc_final: 0.7836 (t80)
  outliers start: 29
  outliers final: 20
  residues processed: 91
  average time/residue: 0.0793
  time to fit residues: 9.7982
Evaluate side-chains
  89 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   15 SER
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0970
   chunk 76 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.129396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.112314 restraints weight = 7389.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.84
r_work: 0.3183 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6376  Z= 0.157
  Angle     :  0.543   6.716   8678  Z= 0.280
  Chirality :  0.037   0.120    982
  Planarity :  0.005   0.052   1058
  Dihedral  :  3.881  13.082    900
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  :  9.41 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.99 (0.29), residues: 794
  helix:  2.13 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop :  0.97 (0.69), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 126 
 TYR   0.011   0.001   TYR A  25 
 PHE   0.010   0.001   PHE A  14 
 TRP   0.013   0.001   TRP B 138 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6376)
  covalent geometry    : angle       0.54266 ( 8678)
  hydrogen bonds       : bond        0.04255 (  564)
  hydrogen bonds       : angle       3.83094 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   96 TRP cc_start: 0.6822 (m100) cc_final: 0.6462 (m100)
REVERT: A  190 GLU cc_start: 0.7851 (pm20) cc_final: 0.7521 (pt0)
REVERT: A  270 GLU cc_start: 0.7705 (mm-30) cc_final: 0.6662 (mp0)
REVERT: A  340 PHE cc_start: 0.8204 (t80) cc_final: 0.7805 (t80)
REVERT: B   96 TRP cc_start: 0.6877 (m100) cc_final: 0.6484 (m100)
REVERT: B  190 GLU cc_start: 0.7828 (pm20) cc_final: 0.7510 (pt0)
REVERT: B  270 GLU cc_start: 0.7748 (mm-30) cc_final: 0.6686 (mp0)
REVERT: B  305 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7879 (mm)
REVERT: B  340 PHE cc_start: 0.8217 (t80) cc_final: 0.7825 (t80)
  outliers start: 27
  outliers final: 22
  residues processed: 92
  average time/residue: 0.0790
  time to fit residues: 9.9808
Evaluate side-chains
  91 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   15 SER
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0070
   chunk 35 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.137850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.119553 restraints weight = 6910.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 1.81
r_work: 0.3663 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6376  Z= 0.151
  Angle     :  0.534   6.684   8678  Z= 0.277
  Chirality :  0.037   0.119    982
  Planarity :  0.005   0.051   1058
  Dihedral  :  3.865  12.952    900
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  :  9.72 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.09 (0.29), residues: 794
  helix:  2.19 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop :  1.11 (0.70), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 126 
 TYR   0.011   0.001   TYR A  25 
 PHE   0.013   0.001   PHE A 250 
 TRP   0.012   0.001   TRP B 138 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6376)
  covalent geometry    : angle       0.53417 ( 8678)
  hydrogen bonds       : bond        0.04225 (  564)
  hydrogen bonds       : angle       3.78707 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   96 TRP cc_start: 0.6943 (m100) cc_final: 0.6672 (m100)
REVERT: A  190 GLU cc_start: 0.7733 (pm20) cc_final: 0.7383 (pt0)
REVERT: A  340 PHE cc_start: 0.8218 (t80) cc_final: 0.7870 (t80)
REVERT: B   96 TRP cc_start: 0.6975 (m100) cc_final: 0.6704 (m100)
REVERT: B  190 GLU cc_start: 0.7791 (pm20) cc_final: 0.7425 (pt0)
REVERT: B  340 PHE cc_start: 0.8248 (t80) cc_final: 0.7904 (t80)
  outliers start: 25
  outliers final: 22
  residues processed: 93
  average time/residue: 0.0764
  time to fit residues: 9.8210
Evaluate side-chains
  95 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   15 SER
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 66 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0870
   overall best weight:    0.5358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.169856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.152282 restraints weight = 6562.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 1.63
r_work: 0.3698 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6376  Z= 0.150
  Angle     :  0.534   6.673   8678  Z= 0.278
  Chirality :  0.037   0.119    982
  Planarity :  0.005   0.051   1058
  Dihedral  :  3.886  13.035    900
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  :  9.88 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.21 (0.30), residues: 794
  helix:  2.24 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop :  1.36 (0.75), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 126 
 TYR   0.011   0.001   TYR A  25 
 PHE   0.010   0.001   PHE A  14 
 TRP   0.012   0.001   TRP A 138 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6376)
  covalent geometry    : angle       0.53438 ( 8678)
  hydrogen bonds       : bond        0.04210 (  564)
  hydrogen bonds       : angle       3.78257 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 TRP cc_start: 0.7007 (m100) cc_final: 0.6757 (m100)
REVERT: A  190 GLU cc_start: 0.7677 (pm20) cc_final: 0.7309 (pt0)
REVERT: A  340 PHE cc_start: 0.8250 (t80) cc_final: 0.7937 (t80)
REVERT: A  372 MET cc_start: 0.7552 (mmt) cc_final: 0.7296 (mmm)
REVERT: B   96 TRP cc_start: 0.6983 (m100) cc_final: 0.6773 (m100)
REVERT: B  190 GLU cc_start: 0.7729 (pm20) cc_final: 0.7358 (pt0)
REVERT: B  270 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6724 (mp0)
REVERT: B  305 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7970 (mm)
REVERT: B  340 PHE cc_start: 0.8261 (t80) cc_final: 0.7925 (t80)
  outliers start: 26
  outliers final: 22
  residues processed: 105
  average time/residue: 0.1212
  time to fit residues: 15.7084
Evaluate side-chains
  93 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   15 SER
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 79 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.135394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.117010 restraints weight = 6997.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 1.83
r_work: 0.3656 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6376  Z= 0.178
  Angle     :  0.562   6.842   8678  Z= 0.292
  Chirality :  0.038   0.122    982
  Planarity :  0.006   0.052   1058
  Dihedral  :  3.947  13.779    900
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 10.03 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.06 (0.30), residues: 794
  helix:  2.12 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop :  1.49 (0.77), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 126 
 TYR   0.012   0.001   TYR A  25 
 PHE   0.011   0.001   PHE A  14 
 TRP   0.014   0.002   TRP B 138 
 HIS   0.005   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 6376)
  covalent geometry    : angle       0.56194 ( 8678)
  hydrogen bonds       : bond        0.04368 (  564)
  hydrogen bonds       : angle       3.87467 ( 1680)

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 TRP cc_start: 0.6987 (m100) cc_final: 0.6710 (m100)
REVERT: A  190 GLU cc_start: 0.7718 (pm20) cc_final: 0.7359 (pt0)
REVERT: A  340 PHE cc_start: 0.8291 (t80) cc_final: 0.7915 (t80)
REVERT: A  372 MET cc_start: 0.7566 (mmt) cc_final: 0.7310 (mmm)
REVERT: B   96 TRP cc_start: 0.6970 (m100) cc_final: 0.6741 (m100)
REVERT: B  190 GLU cc_start: 0.7776 (pm20) cc_final: 0.7420 (pt0)
REVERT: B  270 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6690 (mp0)
REVERT: B  305 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7968 (mm)
REVERT: B  341 SER cc_start: 0.8872 (m) cc_final: 0.8325 (t)
  outliers start: 25
  outliers final: 22
  residues processed: 95
  average time/residue: 0.0608
  time to fit residues: 8.4873
Evaluate side-chains
  99 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 SER
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain B residue   15 SER
Chi-restraints excluded: chain B residue   17 MET
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   71 SER
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  333 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.134868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.116831 restraints weight = 6955.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 1.76
r_work: 0.3651 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.3168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6376  Z= 0.183
  Angle     :  0.569   6.809   8678  Z= 0.295
  Chirality :  0.038   0.125    982
  Planarity :  0.006   0.052   1058
  Dihedral  :  3.968  14.749    900
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 10.65 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.04 (0.30), residues: 794
  helix:  2.08 (0.19), residues: 708
  sheet:  None (None), residues: 0
  loop :  1.71 (0.78), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 126 
 TYR   0.012   0.001   TYR A  25 
 PHE   0.010   0.001   PHE A  14 
 TRP   0.014   0.002   TRP A 138 
 HIS   0.005   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 6376)
  covalent geometry    : angle       0.56908 ( 8678)
  hydrogen bonds       : bond        0.04394 (  564)
  hydrogen bonds       : angle       3.89598 ( 1680)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1509.47 seconds
wall clock time: 26 minutes 46.86 seconds (1606.86 seconds total)