Starting phenix.real_space_refine
on Tue Feb  3 18:52:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w1n_65551/02_2026/9w1n_65551.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w1n_65551/02_2026/9w1n_65551.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w1n_65551/02_2026/9w1n_65551.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w1n_65551/02_2026/9w1n_65551.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w1n_65551/02_2026/9w1n_65551.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w1n_65551/02_2026/9w1n_65551.map"
  }
  resolution = 3.2
  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=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    4094      2.51       5
     N     992      2.21       5
     O    1090      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: 6214
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3107
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 15, 'TRANS': 391}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.88, per 1000 atoms: 0.30
  Number of scatterers: 6214
  At special positions: 0
  Unit cell: (75.53, 113.71, 63.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1090      8.00
     N     992      7.00
     C    4094      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: 0.45
  Conformation dependent library (CDL) restraints added in 318.3 milliseconds
  

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1464

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      87.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 27
    Processing helix  chain 'A' and resid 29 through 34
    Processing helix  chain 'A' and resid 34 through 42
    Processing helix  chain 'A' and resid 45 through 74
      removed outlier: 4.048A  pdb=" N   ASP A  72 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLN A  73 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 96
      removed outlier: 3.523A  pdb=" N   LEU A  79 " --> pdb=" O   SER A  75 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TRP A  96 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 115
      removed outlier: 4.007A  pdb=" N   GLY A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 129
      removed outlier: 3.603A  pdb=" N   CYS A 121 " --> pdb=" O   GLY A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 163
      removed outlier: 3.512A  pdb=" N   TRP A 137 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 164 through 185
      removed outlier: 4.063A  pdb=" N   LEU A 185 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'A' and resid 217 through 222
    Processing helix  chain 'A' and resid 223 through 254
      removed outlier: 4.216A  pdb=" N   TRP A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   GLN A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   PHE A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLU A 254 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 290
    Processing helix  chain 'A' and resid 300 through 320
      removed outlier: 4.355A  pdb=" N   PHE A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 356
      Proline residue:  A 345  - end of helix
    Processing helix  chain 'A' and resid 361 through 391
      removed outlier: 4.073A  pdb=" N   MET A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN A 374 " --> pdb=" O   GLY A 370 " (cutoff:3.500A)
      Proline residue:  A 383  - end of helix
    Processing helix  chain 'A' and resid 392 through 414
    Processing helix  chain 'A' and resid 415 through 417
      No H-bonds generated for 'chain 'A' and resid 415 through 417'
    Processing helix  chain 'B' and resid 6 through 27
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 34 through 42
    Processing helix  chain 'B' and resid 45 through 74
      removed outlier: 4.048A  pdb=" N   ASP B  72 " --> pdb=" O   GLY B  68 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   GLN B  73 " --> pdb=" O   VAL B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 96
      removed outlier: 3.523A  pdb=" N   LEU B  79 " --> pdb=" O   SER B  75 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TRP B  96 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 115
      removed outlier: 4.007A  pdb=" N   GLY B 115 " --> pdb=" O   GLY B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 129
      removed outlier: 3.604A  pdb=" N   CYS B 121 " --> pdb=" O   GLY B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 163
      removed outlier: 3.512A  pdb=" N   TRP B 137 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      Proline residue:  B 153  - end of helix
    Processing helix  chain 'B' and resid 164 through 185
      removed outlier: 4.063A  pdb=" N   LEU B 185 " --> pdb=" O   PHE B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 194
    Processing helix  chain 'B' and resid 217 through 222
    Processing helix  chain 'B' and resid 223 through 254
      removed outlier: 4.216A  pdb=" N   TRP B 227 " --> pdb=" O   SER B 223 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   GLN B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   PHE B 249 " --> pdb=" O   ASP B 245 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLU B 254 " --> pdb=" O   PHE B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 290
    Processing helix  chain 'B' and resid 300 through 320
      removed outlier: 4.355A  pdb=" N   PHE B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 356
      Proline residue:  B 345  - end of helix
    Processing helix  chain 'B' and resid 361 through 391
      removed outlier: 4.073A  pdb=" N   MET B 372 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASN B 374 " --> pdb=" O   GLY B 370 " (cutoff:3.500A)
      Proline residue:  B 383  - end of helix
    Processing helix  chain 'B' and resid 392 through 414
    Processing helix  chain 'B' and resid 415 through 417
      No H-bonds generated for 'chain 'B' and resid 415 through 417'

    523 hydrogen bonds defined for protein.
    1557 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: 0.85

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1806
        1.34 -     1.46: 1419
        1.46 -     1.58: 3101
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6388
  Sorted by residual:
  bond pdb=" CA  VAL B 100 "
       pdb=" C   VAL B 100 "
    ideal  model  delta    sigma   weight residual
    1.520  1.541 -0.021 8.80e-03 1.29e+04 5.70e+00
  bond pdb=" CA  VAL A 100 "
       pdb=" C   VAL A 100 "
    ideal  model  delta    sigma   weight residual
    1.520  1.540 -0.020 8.80e-03 1.29e+04 5.20e+00
  bond pdb=" CG  LEU B 304 "
       pdb=" CD1 LEU B 304 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.56e+00
  bond pdb=" CG  LEU A 304 "
       pdb=" CD1 LEU A 304 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.53e+00
  bond pdb=" CB  ILE A 352 "
       pdb=" CG2 ILE A 352 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.41e+00
  ... (remaining 6383 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 8367
        2.24 -     4.47: 267
        4.47 -     6.71: 44
        6.71 -     8.94: 12
        8.94 -    11.18: 4
  Bond angle restraints: 8694
  Sorted by residual:
  angle pdb=" N   TRP B 118 "
        pdb=" CA  TRP B 118 "
        pdb=" C   TRP B 118 "
      ideal   model   delta    sigma   weight residual
     109.81  117.40   -7.59 2.21e+00 2.05e-01 1.18e+01
  angle pdb=" N   TRP A 118 "
        pdb=" CA  TRP A 118 "
        pdb=" C   TRP A 118 "
      ideal   model   delta    sigma   weight residual
     109.81  117.37   -7.56 2.21e+00 2.05e-01 1.17e+01
  angle pdb=" C   THR B  99 "
        pdb=" N   VAL B 100 "
        pdb=" CA  VAL B 100 "
      ideal   model   delta    sigma   weight residual
     120.24  122.31   -2.07 6.30e-01 2.52e+00 1.08e+01
  angle pdb=" CA  LEU B 305 "
        pdb=" CB  LEU B 305 "
        pdb=" CG  LEU B 305 "
      ideal   model   delta    sigma   weight residual
     116.30  105.12   11.18 3.50e+00 8.16e-02 1.02e+01
  angle pdb=" CA  LEU A 305 "
        pdb=" CB  LEU A 305 "
        pdb=" CG  LEU A 305 "
      ideal   model   delta    sigma   weight residual
     116.30  105.12   11.18 3.50e+00 8.16e-02 1.02e+01
  ... (remaining 8689 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.15: 3434
       15.15 -    30.30: 140
       30.30 -    45.45: 36
       45.45 -    60.60: 4
       60.60 -    75.75: 4
  Dihedral angle restraints: 3618
    sinusoidal: 1312
      harmonic: 2306
  Sorted by residual:
  dihedral pdb=" CA  ILE B 252 "
           pdb=" C   ILE B 252 "
           pdb=" N   GLN B 253 "
           pdb=" CA  GLN B 253 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.02  -17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ILE A 252 "
           pdb=" C   ILE A 252 "
           pdb=" N   GLN A 253 "
           pdb=" CA  GLN A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.05  -17.95     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  PRO A 119 "
           pdb=" C   PRO A 119 "
           pdb=" N   PRO A 120 "
           pdb=" CA  PRO A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.75   16.25     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 3615 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 827
       0.069 -    0.138: 143
       0.138 -    0.207: 12
       0.207 -    0.276: 0
       0.276 -    0.345: 2
  Chirality restraints: 984
  Sorted by residual:
  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   -2.28   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" CB  VAL A  34 "
            pdb=" CA  VAL A  34 "
            pdb=" CG1 VAL A  34 "
            pdb=" CG2 VAL A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" CA  LEU A 382 "
            pdb=" N   LEU A 382 "
            pdb=" C   LEU A 382 "
            pdb=" CB  LEU A 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.84e-01
  ... (remaining 981 not shown)

  Planarity restraints: 1064
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 344 "    0.050 5.00e-02 4.00e+02   7.54e-02 9.11e+00
        pdb=" N   PRO B 345 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B 345 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 345 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 344 "   -0.050 5.00e-02 4.00e+02   7.52e-02 9.04e+00
        pdb=" N   PRO A 345 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO A 345 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 345 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 119 "    0.040 5.00e-02 4.00e+02   6.01e-02 5.77e+00
        pdb=" N   PRO B 120 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 120 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 120 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1061 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1636
        2.79 -     3.32: 5925
        3.32 -     3.85: 11188
        3.85 -     4.37: 12755
        4.37 -     4.90: 21869
  Nonbonded interactions: 53373
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 317 "
            pdb=" OG1 THR B 321 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   LEU A 317 "
            pdb=" OG1 THR A 321 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OH  TYR B   6 "
            pdb=" O   TRP B 128 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OH  TYR A   6 "
            pdb=" O   TRP A 128 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OG  SER B  22 "
            pdb=" OG  SER B 144 "
     model   vdw
     2.295 3.040
  ... (remaining 53368 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:             4.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.160
  Find NCS groups from input model:        0.030
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
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      :  0.007   0.069   6388  Z= 0.285
  Angle     :  0.952  11.178   8694  Z= 0.503
  Chirality :  0.054   0.345    984
  Planarity :  0.009   0.075   1064
  Dihedral  :  9.962  75.748   2154
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  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: -3.30 (0.23), residues: 806
  helix: -1.88 (0.15), residues: 658
  sheet:  None (None), residues: 0
  loop : -2.58 (0.45), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 126 
 TYR   0.030   0.003   TYR B 343 
 PHE   0.030   0.003   PHE A 349 
 TRP   0.040   0.003   TRP A 138 
 HIS   0.006   0.002   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 ( 6388)
  covalent geometry    : angle       0.95167 ( 8694)
  hydrogen bonds       : bond        0.10710 (  523)
  hydrogen bonds       : angle       6.35378 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.131 
Fit side-chains
REVERT: B  250 PHE cc_start: 0.7346 (t80) cc_final: 0.7117 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1165
  time to fit residues: 17.5370
Evaluate side-chains
  76 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A 374 ASN
A 390 HIS
B 374 ASN
B 390 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.196517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.178363 restraints weight = 7588.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.4130 rms_B_bonded: 1.66
r_work: 0.4009 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3889 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6388  Z= 0.164
  Angle     :  0.615   8.344   8694  Z= 0.320
  Chirality :  0.041   0.139    984
  Planarity :  0.006   0.059   1064
  Dihedral  :  4.691  14.789    866
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  7.47 %
    Favored  : 92.23 %
  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: -0.57 (0.27), residues: 806
  helix:  0.04 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.78 (0.47), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 166 
 TYR   0.009   0.001   TYR B 343 
 PHE   0.016   0.002   PHE B 103 
 TRP   0.023   0.002   TRP A 138 
 HIS   0.001   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6388)
  covalent geometry    : angle       0.61483 ( 8694)
  hydrogen bonds       : bond        0.04736 (  523)
  hydrogen bonds       : angle       4.59816 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  250 PHE cc_start: 0.7683 (t80) cc_final: 0.7461 (t80)
REVERT: B  286 ARG cc_start: 0.7042 (ttm-80) cc_final: 0.6797 (ttm-80)
  outliers start: 2
  outliers final: 2
  residues processed: 88
  average time/residue: 0.0787
  time to fit residues: 8.9185
Evaluate side-chains
  79 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain B residue  392 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4260 r_free = 0.4260 target = 0.192965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.174499 restraints weight = 7473.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.4085 rms_B_bonded: 1.65
r_work: 0.3968 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3851 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6388  Z= 0.176
  Angle     :  0.603   8.166   8694  Z= 0.310
  Chirality :  0.041   0.142    984
  Planarity :  0.006   0.051   1064
  Dihedral  :  4.460  13.574    866
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  9.15 %
    Favored  : 89.94 %
  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:  0.61 (0.28), residues: 806
  helix:  0.92 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.68 (0.45), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 166 
 TYR   0.009   0.002   TYR B 343 
 PHE   0.016   0.002   PHE A 250 
 TRP   0.019   0.002   TRP A 138 
 HIS   0.001   0.000   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6388)
  covalent geometry    : angle       0.60259 ( 8694)
  hydrogen bonds       : bond        0.04683 (  523)
  hydrogen bonds       : angle       4.34058 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.149 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 80
  average time/residue: 0.0600
  time to fit residues: 6.5256
Evaluate side-chains
  67 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  392 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    0.1980
   chunk 40 optimal weight:    3.9990
   chunk 42 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 3 optimal weight:    0.3980
   chunk 30 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4295 r_free = 0.4295 target = 0.196092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.178271 restraints weight = 7459.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.4124 rms_B_bonded: 1.60
r_work: 0.4008 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3890 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6388  Z= 0.147
  Angle     :  0.566   7.076   8694  Z= 0.293
  Chirality :  0.041   0.247    984
  Planarity :  0.005   0.049   1064
  Dihedral  :  4.270  12.909    866
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.37 %
    Favored  : 88.41 %
  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:  1.26 (0.29), residues: 806
  helix:  1.38 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.67 (0.45), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 166 
 TYR   0.010   0.001   TYR A  25 
 PHE   0.014   0.002   PHE A 250 
 TRP   0.015   0.001   TRP A 138 
 HIS   0.001   0.000   HIS B 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6388)
  covalent geometry    : angle       0.56559 ( 8694)
  hydrogen bonds       : bond        0.04409 (  523)
  hydrogen bonds       : angle       4.10318 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8167 (m110) cc_final: 0.7897 (m110)
REVERT: A  166 ARG cc_start: 0.6603 (mtm110) cc_final: 0.6182 (ttm-80)
REVERT: A  250 PHE cc_start: 0.7697 (t80) cc_final: 0.7470 (t80)
REVERT: B   27 ASN cc_start: 0.8144 (m110) cc_final: 0.7903 (m110)
REVERT: B  250 PHE cc_start: 0.7664 (t80) cc_final: 0.7460 (t80)
  outliers start: 8
  outliers final: 6
  residues processed: 86
  average time/residue: 0.0604
  time to fit residues: 7.0814
Evaluate side-chains
  74 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  392 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 72 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   chunk 12 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 = 0.4264 r_free = 0.4264 target = 0.193504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.174638 restraints weight = 7662.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.4092 rms_B_bonded: 1.70
r_work: 0.3973 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3852 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6388  Z= 0.162
  Angle     :  0.583  11.327   8694  Z= 0.297
  Chirality :  0.042   0.263    984
  Planarity :  0.005   0.049   1064
  Dihedral  :  4.225  13.451    866
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.13 %
    Favored  : 87.50 %
  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:  1.56 (0.29), residues: 806
  helix:  1.59 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.57 (0.45), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 166 
 TYR   0.010   0.001   TYR A  25 
 PHE   0.017   0.002   PHE B 338 
 TRP   0.014   0.001   TRP A 138 
 HIS   0.001   0.000   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6388)
  covalent geometry    : angle       0.58290 ( 8694)
  hydrogen bonds       : bond        0.04458 (  523)
  hydrogen bonds       : angle       4.10269 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8219 (m110) cc_final: 0.7914 (m110)
REVERT: B   27 ASN cc_start: 0.8178 (m110) cc_final: 0.7917 (m110)
REVERT: B  250 PHE cc_start: 0.7695 (t80) cc_final: 0.7472 (t80)
  outliers start: 9
  outliers final: 5
  residues processed: 82
  average time/residue: 0.0721
  time to fit residues: 7.9678
Evaluate side-chains
  75 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  392 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4255 r_free = 0.4255 target = 0.192524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.173893 restraints weight = 7513.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 1.67
r_work: 0.3960 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3840 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6388  Z= 0.166
  Angle     :  0.586  10.058   8694  Z= 0.299
  Chirality :  0.041   0.195    984
  Planarity :  0.006   0.050   1064
  Dihedral  :  4.220  14.767    866
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.89 %
    Favored  : 86.59 %
  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:  1.67 (0.29), residues: 806
  helix:  1.65 (0.20), residues: 668
  sheet:  None (None), residues: 0
  loop : -1.58 (0.45), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 166 
 TYR   0.010   0.001   TYR B  25 
 PHE   0.019   0.002   PHE B 338 
 TRP   0.014   0.001   TRP A 138 
 HIS   0.001   0.000   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6388)
  covalent geometry    : angle       0.58599 ( 8694)
  hydrogen bonds       : bond        0.04457 (  523)
  hydrogen bonds       : angle       4.10646 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8240 (m110) cc_final: 0.7939 (m110)
REVERT: B   10 ARG cc_start: 0.6197 (mtt180) cc_final: 0.5847 (mtt180)
REVERT: B   27 ASN cc_start: 0.8203 (m110) cc_final: 0.7965 (m110)
REVERT: B  250 PHE cc_start: 0.7709 (t80) cc_final: 0.7476 (t80)
  outliers start: 10
  outliers final: 7
  residues processed: 85
  average time/residue: 0.0612
  time to fit residues: 7.1290
Evaluate side-chains
  80 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  392 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0570
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.4252 r_free = 0.4252 target = 0.192279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.173731 restraints weight = 7536.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 1.66
r_work: 0.3957 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3841 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.3230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6388  Z= 0.165
  Angle     :  0.591   9.511   8694  Z= 0.300
  Chirality :  0.041   0.188    984
  Planarity :  0.006   0.050   1064
  Dihedral  :  4.207  15.436    866
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.11 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.82 (0.29), residues: 806
  helix:  1.78 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.60 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 166 
 TYR   0.009   0.001   TYR A  25 
 PHE   0.020   0.002   PHE B 338 
 TRP   0.014   0.001   TRP B 138 
 HIS   0.001   0.000   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6388)
  covalent geometry    : angle       0.59092 ( 8694)
  hydrogen bonds       : bond        0.04449 (  523)
  hydrogen bonds       : angle       4.09919 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8279 (m110) cc_final: 0.8031 (m110)
REVERT: A  307 MET cc_start: 0.7300 (mtm) cc_final: 0.6882 (mtt)
REVERT: B  169 LEU cc_start: 0.5895 (tp) cc_final: 0.4930 (tp)
  outliers start: 7
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0529
  time to fit residues: 6.1461
Evaluate side-chains
  77 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  392 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 133 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.191485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.172932 restraints weight = 7601.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 1.67
r_work: 0.3951 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3831 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6388  Z= 0.170
  Angle     :  0.601   9.624   8694  Z= 0.305
  Chirality :  0.041   0.169    984
  Planarity :  0.006   0.050   1064
  Dihedral  :  4.227  16.051    866
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.11 %
    Favored  : 85.21 %
  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:  1.90 (0.29), residues: 806
  helix:  1.83 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.58 (0.45), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 166 
 TYR   0.009   0.001   TYR A  25 
 PHE   0.021   0.002   PHE B 338 
 TRP   0.014   0.001   TRP A 138 
 HIS   0.001   0.000   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6388)
  covalent geometry    : angle       0.60150 ( 8694)
  hydrogen bonds       : bond        0.04475 (  523)
  hydrogen bonds       : angle       4.11682 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8226 (m110) cc_final: 0.7776 (m110)
  outliers start: 11
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0592
  time to fit residues: 6.5058
Evaluate side-chains
  76 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  392 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   chunk 77 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 23 optimal weight:    0.2980
   chunk 54 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.193568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.175199 restraints weight = 7613.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.4094 rms_B_bonded: 1.67
r_work: 0.3975 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3856 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6388  Z= 0.151
  Angle     :  0.589   9.161   8694  Z= 0.298
  Chirality :  0.040   0.164    984
  Planarity :  0.006   0.051   1064
  Dihedral  :  4.199  16.225    866
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 13.41 %
    Favored  : 85.37 %
  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:  2.09 (0.30), residues: 806
  helix:  1.98 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.54 (0.44), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 166 
 TYR   0.009   0.001   TYR A  24 
 PHE   0.019   0.002   PHE B 338 
 TRP   0.013   0.001   TRP A 138 
 HIS   0.001   0.000   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6388)
  covalent geometry    : angle       0.58860 ( 8694)
  hydrogen bonds       : bond        0.04370 (  523)
  hydrogen bonds       : angle       4.04995 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8279 (m110) cc_final: 0.8012 (m110)
  outliers start: 8
  outliers final: 7
  residues processed: 78
  average time/residue: 0.0708
  time to fit residues: 7.4634
Evaluate side-chains
  78 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  392 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0570
   chunk 61 optimal weight:    0.7980
   chunk 68 optimal weight:   50.0000
   chunk 56 optimal weight:    0.4980
   chunk 60 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.4263 r_free = 0.4263 target = 0.193277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.175331 restraints weight = 7507.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.4093 rms_B_bonded: 1.62
r_work: 0.3975 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3859 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6388  Z= 0.159
  Angle     :  0.601   9.375   8694  Z= 0.304
  Chirality :  0.041   0.160    984
  Planarity :  0.006   0.053   1064
  Dihedral  :  4.193  16.029    866
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.26 %
    Favored  : 85.37 %
  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:  2.13 (0.29), residues: 806
  helix:  2.01 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.54 (0.44), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 166 
 TYR   0.009   0.001   TYR B  24 
 PHE   0.016   0.002   PHE B 338 
 TRP   0.013   0.001   TRP B 138 
 HIS   0.001   0.000   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6388)
  covalent geometry    : angle       0.60114 ( 8694)
  hydrogen bonds       : bond        0.04399 (  523)
  hydrogen bonds       : angle       4.04899 ( 1557)

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

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

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1612 Ramachandran restraints generated.
    806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   27 ASN cc_start: 0.8272 (m110) cc_final: 0.8021 (m110)
REVERT: B  159 LEU cc_start: 0.6766 (mp) cc_final: 0.6502 (mt)
  outliers start: 9
  outliers final: 8
  residues processed: 82
  average time/residue: 0.0726
  time to fit residues: 7.9389
Evaluate side-chains
  81 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain B residue  176 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  392 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.188876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.171292 restraints weight = 7529.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 1.59
r_work: 0.3945 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3830 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6388  Z= 0.189
  Angle     :  0.630   9.898   8694  Z= 0.320
  Chirality :  0.042   0.154    984
  Planarity :  0.006   0.053   1064
  Dihedral  :  4.270  16.848    866
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.87 %
    Favored  : 85.06 %
  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:  1.96 (0.29), residues: 806
  helix:  1.88 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.61 (0.44), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 166 
 TYR   0.010   0.001   TYR A  25 
 PHE   0.024   0.002   PHE B 338 
 TRP   0.014   0.001   TRP A 138 
 HIS   0.002   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 6388)
  covalent geometry    : angle       0.62996 ( 8694)
  hydrogen bonds       : bond        0.04590 (  523)
  hydrogen bonds       : angle       4.17055 ( 1557)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1254.46 seconds
wall clock time: 22 minutes 12.42 seconds (1332.42 seconds total)